Vaguery + molecular-design   48

[1802.03548] Constructing first-principles phase diagrams of amorphous LixSi using machine-learning-assisted sampling with an evolutionary algorithm
The atomistic modeling of amorphous materials requires structure sizes and sampling statistics that are challenging to achieve with first-principles methods. Here, we propose a methodology to speed up the sampling of amorphous and disordered materials using a combination of a genetic algorithm and a specialized machine-learning potential based on artificial neural networks (ANN). We show for the example of the amorphous LiSi alloy that around 1,000 first-principles calculations are sufficient for the ANN potential assisted sampling of low-energy atomic configurations in the entire amorphous LixSi phase space. The obtained phase diagram is validated by comparison with the results from an extensive sampling of LixSi configurations using molecular dynamics simulations and a general ANN potential trained to ~45,000 first-principles calculations. This demonstrates the utility of the approach for the first-principles modeling of amorphous materials.
metaheuristics  materials-science  engineering-design  molecular-design  rather-interesting  simulation 
6 days ago by Vaguery
Supermultiplexed optical imaging and barcoding with engineered polyynes | Nature Methods
Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability. Moreover, we realized optical data storage and identification by combinatorial barcoding, yielding to our knowledge the largest number of distinct spectral barcodes to date. Therefore, these polyynes hold great promise in live-cell imaging and sorting as well as in high-throughput diagnostics and screening.
materials-science  nanotechnology  indistinguishable-from-magic  molecular-design  molecular-biology  to-write-about  rather-interesting 
december 2018 by Vaguery
The Effect of Compositional Context on Synthetic Gene Net- works | bioRxiv
It is well known that synthetic gene expression is highly sensitive to how genetic elements (promoter structure, spacing regions between promoter and cod- ing sequences, ribosome binding sites, etc.) are spatially configured. An important topic that has received far less attention is how the compositional context, or spatial arrangement, of entire genes within a synthetic gene network affects their individual expression levels. In this paper we show, both quantitatively and qualitatively, that compositional context significantly alters transcription levels in synthetic gene networks. We demonstrate that key characteristics of gene induction, such as ultra-sensitivity and dynamic range, strongly depend on compositional context. We postulate that supercoiling can be used to explain this interference and validate this hypothesis through modeling and a series of in vitro supercoiling relaxation experiments. This compo- sitional interference enables a novel form of feedback in synthetic gene networks. We illustrate the use of this feedback by redesigning the toggle switch to incorporate compositional context. We show the context-optimized toggle switch has improved threshold detection and memory properties.
gene-regulatory-networks  biological-engineering  systems-biology  rather-interesting  synthetic-biology  molecular-design  to-write-about  performance-measure 
october 2017 by Vaguery
Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers
Today’s lifeforms are based on informational polymers, namely proteins and nucleic acids. It is thought that simple chemical processes on the early earth could have polymerized monomer units into short random sequences. It is not clear, however, what physical process could have led to the next level—to longer chains having particular sequences that could increase their own concentrations. We study polymers of hydrophobic and polar monomers, such as today’s proteins. We find that even some random sequence short chains can collapse into compact structures in water, with hydrophobic surfaces that can act as primitive catalysts, and that these could elongate other chains. This mechanism explains how random chemical polymerizations could have given rise to longer sequence-dependent protein-like catalytic polymers.
lattice-polymers  biophysics  self-organization  origin-of-life  simulation  rather-interesting  to-write-about  molecular-design  molecular-machinery 
september 2017 by Vaguery
[1702.01994] Polyomino Models of Surface Supramolecular Assembly: Design Constraints and Structural Selectivity
We examine emergent properties of 2D supramolecular networks, using enumeration of configurations formed by interacting dominoes on square lattices as a simple model system. Possible ground states are identified using a convex hull construction in the interaction parameters for nearest-neighbour bonds. We demonstrate how this construction can be used to design interaction parameters which lead to networks with specific properties, including chirality and highly degenerate ground states. We then introduce kinetics as simple local rearrangements. By partitioning the configuration space into smaller sets which satisfy different topological constraints, we can design configurations which are kinetically trapped. By considering heat capacity curves along directions through the convex hull, we also demonstrate design of interacting domino configurations to create tilings robust against temperature induced phase transitions. We discuss extension of this design construction to more complex molecular shapes.
tiling  supramolecular-complexes  biological-engineering  rather-interesting  to-write-about  energy-landscapes  self-assembly  molecular-design  structural-biology  nanotechnology 
september 2017 by Vaguery
[1502.07144] Self-assembly of Active Colloidal Molecules with Dynamic Function
Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not exhibit any form of dynamical activity, the concentration fields resulting from their chemical activity decay as 1/r and produce gradients that attract or repel other colloids depending on their surface chemistry and ambient variables. This results in a non-equilibrium analogue of ionic systems, but with the remarkable novel feature of action-reaction symmetry breaking. We study solutions of such chemically active colloids in dilute conditions when they join up to form molecules via generalized ionic bonds, and discuss how we can achieve structures with time dependent functionality. In particular, we study a molecule that adopts a spontaneous oscillatory pattern of conformations, and another that exhibits a run-and-tumble dynamics similar to bacteria. Our study shows that catalytically active colloids could be used for designing self-assembled structures that posses dynamical functionalities that are determined by their prescribed 3D structures, a strategy that follows the design principle of proteins.
active-matter  self-organization  physics!  emergence  rather-interesting  to-understand  molecular-design 
may 2017 by Vaguery
Chromatin structure shapes the search process of transcription factors | bioRxiv
The diffusion of regulatory proteins within the nucleus plays a crucial role in the dynamics of transcriptional regulation. The standard model assumes a 3D plus 1D diffusion process: regulatory proteins either move freely in solution or slide on DNA. This model however does not considered the 3D structure of chromatin. Here we proposed a multi-scale stochastic model that integrates, for the first time, high-resolution information on chromatin structure as well as DNA-protein interactions. The dynamics of transcription factors was modeled as a slide plus jump diffusion process on a chromatin network based on pair-wise contact maps obtained from high-resolution Hi-C experiments. Our model allowed us to uncover the effects of chromatin structure on transcription factor occupancy profiles and target search times. Finally, we showed that binding sites clustered on few topological associated domains leading to a higher local concentration of transcription factors which could reflect an optimal strategy to efficiently use limited transcriptional resources.
structural-biology  molecular-design  molecular-biology  systems-biology  bioinformatics  it's-more-complicated-than-you-think 
may 2016 by Vaguery
[1505.01215] Binding of transcription factors adapts to resolve information-energy trade-off
We examine the binding of transcription factors to DNA in terms of an information transfer problem. The input of the noisy channel is the biophysical signal of a factor bound to a DNA site, and the output is a distribution of probable DNA sequences at this site. This task involves an inherent tradeoff between the information gain and the energetics of the binding interaction - high binding energies provide higher information gain but hinder the dynamics of the system as factors are bound too tightly. We show that adaptation of the binding interaction towards increasing information transfer under a general energy constraint implies that the information gain per specific binding energy at each base-pair is maximized. We analyze hundreds of prokaryote and eukaryote transcription factors from various organisms to evaluate the discrimination energies. We find that, in accordance with our theoretical argument, binding energies nearly maximize the information gain per energy. This work suggests the adaptation of information gain as a generic design principle of molecular recognition systems.
molecular-design  molecular-biology  information-theory  theoretical-biology  adaptationism  robustness 
march 2016 by Vaguery
[1505.01023] Classical Liquids in Fractal Dimension
We introduce fractal liquids by generalizing classical liquids of integer dimensions d=1,2,3 to a fractal dimension df. The particles composing the liquid are fractal objects and their configuration space is also fractal, with the same non-integer dimension. Realizations of our generic model system include microphase separated binary liquids in porous media, and highly branched liquid droplets confined to a fractal polymer backbone in a gel. Here we study the thermodynamics and pair correlations of fractal liquids by computer simulation and semi-analytical statistical mechanics. Our results are based on a model where fractal hard spheres move on a near-critical percolating lattice cluster. The predictions of the fractal Percus-Yevick liquid integral equation compare well with our simulation results.
fluid-dynamics  but-different  fractals  physics  simulation  percolation  molecular-design  rather-interesting  nonlinear-dynamics  condensed-matter 
september 2015 by Vaguery
[1506.08611] Energy landscapes for the self-assembly of supramolecular polyhedra
We develop a mathematical model for the energy landscape of polyhedral supramolecular cages recently synthesized by self-assembly [Sun et al., Science 2010]. Our model includes two essential features of the experiment: (i) geometry of the organic ligands and metallic ions; and (ii) combinatorics. The molecular geometry is used to introduce an energy that favors square-planar vertices (modeling Pd2+ ions) and bent edges with one of two preferred opening angles (modeling boomerang-shaped ligands of two types). The combinatorics of the model involve 2-colorings of edges of polyhedra with 4-valent vertices. The set of such 2-colorings, quotiented by the octahedral symmetry group, has a natural graph structure, and is called the combinatorial configuration space. The energy landscape of our model is the energy of each state in the combinatorial configuration space.
The challenge in the computation of the energy landscape is a combinatorial explosion in the number of 2-colorings of edges. We describe sampling methods based on the symmetries of the configurations and connectivity of the configuration graph. When the two preferred opening angles encompass the geometrically ideal angle, the energy landscape exhibits a very low-energy minimum for the most symmetric configuration at equal mixing of the two angles, even when the average opening angle does not match the ideal angle.
statistical-mechanics  energy-landscapes  molecular-design  engineering-design  rather-interesting  models-and-modes  nudge-targets  nonlinear-dynamics 
august 2015 by Vaguery
[1401.1491] Gradient-Driven Molecule Construction: An Inverse Approach Applied to the Design of Small-Molecule Fixating Catalysts
Rational design of molecules and materials usually requires extensive screening of molecular structures for the desired property. The inverse approach to deduce a structure for a predefined property would be highly desirable, but is, unfortunately, not well-defined. However, feasible strategies for such an inverse design process may be successfully developed for specific purposes. We discuss options for calculating 'jacket' potentials that fulfill a predefined target requirement - a concept that we recently introduced [T. Weymuth, M. Reiher, MRS Proceediungs, 2013, 1524, DOI:10.1557/opl.2012.1764]. We consider the case of small-molecule activating transition metal catalysts. As a target requirement we choose the vanishing geometry gradients on all atoms of a subsystem consisting of a metal center binding the small molecule to be activated. The jacket potential can be represented within a full quantum model or by a sequence of approximations of which a field of electrostatic point charges is the simplest. In a second step, the jacket potential needs to be replaced by a chemically viable chelate-ligand structure for which the geometry gradients on all of its atoms are also required to vanish. In order to analyze the feasibility of this approach, we dissect a known dinitrogen-fixating catalyst to study possible design strategies that must eventually produce the known catalyst.
engineering-design  chemistry  cheminformatics  molecular-design  algorithms  generative-methods  nudge-targets  consider:performance-measures 
february 2015 by Vaguery
[1310.5091] Synchronization as a unifying mechanism for protein folding
Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an accurate description of kinetics and thermodynamics for such phenomena has not yet been identified. This study introduces the hypothesis that the synchronization of the peptide plane oscillatory movements throughout the backbone must also play a key role in the folding mechanism. Based on that, we draw a parallel between the folding process and the dynamics for a network of coupled oscillators described by the Kuramoto model. The amino acid coupling may explain the mean-field character of the force that propels an amino acid sequence into a structure through self-organization. Thus, the pattern of synchronized cluster formation and growing helps to solve the Levinthal's paradox.Synchronization may also help us to understand the success of homology structural modeling, allosteric effect, and the mechanism responsible for the recognition of odorants by olfactory receptors.
protein-folding  molecular-design  coupled-oscillators  simulation  coordination  rather-interesting  nudge-targets  consider:detectors 
november 2014 by Vaguery
Systematic Imaging Reveals Features of Localized mRNAs and Their Changing Subcellular Destinations in Development | bioRxiv
The asymmetric distribution of cytoplasmic components by mRNA localization is critical for eukaryotic cells and affects large numbers of transcripts. How such global subcellular localization of mRNAs is regulated is still unknown. We combined transcriptomics and systematic imaging to determine tissue-specific expression and subcellular localizations of 5862 mRNAs during Drosophila oogenesis. While the transcriptome is stable and alternative splicing and polyadenylation is rare, cytoplasmic localization of mRNAs is widespread. Localized mRNAs have distinct gene features and diverge in expression level, 3'UTR length and sequence conservation. We show that intracellular localization of mRNAs depends on an intact microtubule cytoskeleton and that specifically the posterior enrichment requires the localization of oskar mRNA to the posterior cortex. Using cross-tissue comparison we revealed that the localization landscape differs substantially between epithelial, germline and embryonic cells and the localization status of mRNAs also changes considerably within the oocyte over the course of oogenesis.
evo-devo  developmental-biology  experiment  molecular-biology  visualization  dynamical-systems  rather-interesting  molecular-design  biological-engineering  self-organization  design-patterns 
november 2014 by Vaguery
Scaling properties of evolutionary paths in a biophysical model of protein adaptation | bioRxiv
The enormous size and complexity of genotypic sequence space frequently requires consideration of coarse-grained sequences in empirical models. We develop scaling relations to quantify the effect of this coarse-graining on properties of fitness landscapes and evolutionary paths. We first consider evolution on a simple Mount Fuji fitness landscape, focusing on how the length and predictability of evolutionary paths scale with the coarse-grained sequence length and number of alleles. We obtain simple scaling relations for both the weak- and strong-selection limits, with a non-trivial crossover regime at intermediate selection strengths. We apply these results to evolution on a biophysical fitness landscape designed to describe how proteins evolve new binding interactions while maintaining their folding stability. We combine numerical calculations for coarse-grained protein sequences with the scaling relations to obtain quantitative properties of the model for realistic binding interfaces and a full amino acid alphabet.
fitness-landscapes  Kauffmania  theoretical-biology  molecular-design  complexology  nudge-targets  multiscale-representations?  approximation 
october 2014 by Vaguery
[1401.4475] Controlled self-assembly of periodic and aperiodic cluster crystals
Soft particles are known to overlap and form stable clusters that self-assemble into periodic crystalline phases with density-independent lattice constants. We use molecular dynamics simulations in two dimensions to demonstrate that, through a judicious design of an isotropic pair potential, one can control the ordering of the clusters and generate a variety of phases, including decagonal and dodecagonal quasicrystals. Our results confirm analytical predictions based on a mean-field approximation, providing insight into the stabilization of quasicrystals in soft macromolecular systems, and suggesting a practical approach for their controlled self-assembly in laboratory realizations using synthesized soft-matter particles.
molecular-design  self-organization  self-assembly  nanotechnology  simulation  condensed-matter  pattern-formation  nudge-targets  consider:diversity-of-particles 
september 2014 by Vaguery
[1403.2269] Virus Assembly on a Membrane is Facilitated by Membrane Microdomains
For many viruses assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials applications. To this end, we have performed molecular dynamics simulations on a coarse-grained model that describes virus assembly on a fluctuating lipid membrane. Our simulations show that the membrane can promote association of adsorbed subunits through dimensional reduction, but also can introduce barriers that inhibit complete assembly. We find several mechanisms, including one not anticipated by equilibrium theories, by which membrane microdomains, such as lipid rafts, can enhance assembly by reducing these barriers. We show how this predicted mechanism can be experimentally tested. Furthermore, the simulations demonstrate that assembly and budding depend crucially on the system dynamics via multiple timescales related to membrane deformation, protein diffusion, association, and adsorption onto the membrane.
structural-biology  simulation  membrane-biochemistry  self-assembly  molecular-design  molecular-machinery  well-duh  it's-crowded-inside-a-cell 
april 2014 by Vaguery
[1311.0684] Uniform generation of RNA-RNA interaction structures of fixed topological genus
Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of fixed topological genus. The bijection allows to either reduce the topological genus of a bicellular map directly, or to lose connectivity by decomposing the complex into a pair of single stranded RNA structures. Our main result is proved bijectively. It provides an explicit algorithm of how to rewire the corresponding complexes and an unambiguous decomposition grammar. Using the concept of genus induction, we construct bicellular maps of fixed topological genus g uniformly in linear time. We present various statistics on these topological RNA complexes and compare our findings with biological complexes. Furthermore we show how to construct loop-energy based complexes using our decomposition grammar.
bioinformatics  molecular-design  RNA  macromolecular-dynamics  nudge-targets  algorithms 
april 2014 by Vaguery
[1401.6866] Unconventional ordering behavior of semi-flexible polymers in dense brushes under compression
Using a coarse-grained bead-spring model for semi-flexible macromolecules forming a polymer brush, structure and dynamics of the polymers is investigated, varying chain stiffness and grafting density. The anchoring condition for the grafted chains is chosen such that their first bonds are oriented along the normal to the substrate plane.
Compression of such a semi-flexible brush by a planar piston is observed to be a two-stage process: for small compressions the chains contract by "buckling" deformation whereas for larger compression the chains exhibit a collective (almost uniform) bending deformation. Thus, the stiff polymer brush undergoes a 2-nd order phase transition of collective bond reorientation. The pressure, required to keep the stiff brush at a given degree of compression, is thereby significantly smaller than for an otherwise identical brush made of entirely flexible polymer chains! While both the brush height and the chain linear dimension in the z-direction perpendicular to the substrate increase monotonically with increasing chain stiffness, lateral (xy) chain linear dimensions exhibit a maximum at intermediate chain stiffness. Increasing the grafting density leads to a strong decrease of these lateral dimensions, compatible with an exponential decay. Also the recovery kinetics after removal of the compressing piston is studied, and found to follow a power-law / exponential decay with time.
A simple mean-field theoretical consideration, accounting for the buckling/bending behavior of semi-flexible polymer brushes under compression, is suggested.
simulation  molecular-design  nanotechnology  condensed-matter  phase-transitions  emergence  nudge-targets  consider:heterogeneity 
april 2014 by Vaguery
[1311.1178] When are rough surfaces sticky?
At the molecular scale there are strong attractive interactions between surfaces, yet few macroscopic surfaces are sticky. Extensive simulations of contact by adhesive surfaces with roughness on nanometer to micrometer scales are used to determine how roughness reduces the area where atoms contact and thus weakens adhesion. The material properties, adhesive strength and roughness parameters are varied by orders of magnitude. In all cases the area of atomic contact rises linearly with load, and the prefactor rises linearly with adhesive strength for weak interactions. Above a threshold adhesive strength, the prefactor changes sign, the surfaces become sticky and a finite force is required to separate them. A parameter-free analytic theory is presented that describes changes in these numerical results over up to five orders of magnitude in load. It relates the threshold strength to roughness and material properties, explaining why most macroscopic surfaces do not stick. The numerical results are qualitatively and quantitatively inconsistent with classical theories based on the Greenwood-Williamson approach that neglect the range of adhesion and do not include asperity interactions.
physics  molecular-design  simulation  nudge-targets  consider:surface-geometry 
april 2014 by Vaguery
[1310.7019] Simulations of imaging of the local density of states by charged probe technique for resonant cavities
We simulate scanning probe imaging of the local density of states related to scattering Fermi level wave functions inside a resonant cavity. We calculate potential landscape within the cavity taking into account the Coulomb charge of the probe and its screening by deformation of the two-dimensional electron gas using the local density approximation. Approximation of the tip potential by a Lorentz function is discussed. The electron transfer problem is solved with a finite difference approach. We look for stable work points for the extraction of the local density of states from conductance maps. We find that conductance maps are highly correlated with the local density of states when the Fermi energy level enters into Fano resonance with states localized within the cavity. Generally outside resonances the correlation between the local density of states and conductance maps is low.
nanotechnology  molecular-design  simulation  electromagnetism  nudge-targets  consider:inverse-problem  consider:robustness 
march 2014 by Vaguery
[1312.0075] Sequence-dependent folding landscapes of adenine riboswitch aptamers
Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a combination of all atom molecular dynamics and coarse-grained model simulations we studied the response of adenine (A) binding add and pbuE A-riboswitches to mechanical force. The two riboswitches contain a structurally similar three-way junction formed by three paired helices, P1, P2, and P3, but carry out different functions. Using pulling simulations, with structures generated in MD simulations, we show that after P1 rips the dominant unfolding pathway in add A-riboswitch is the rupture of P2 followed by unraveling of P3. In the pbuE A-riboswitch, after P1 unfolds P3 ruptures ahead of P2. The order of unfolding of the helices, which is in accord with single molecule pulling experiments, is determined by the relative stabilities of the individual helices. Our results show that the stability of isolated helices determines the order of assembly and response to force in these non-coding regions. We use the simulated free energy profile for pbuE A-riboswitch to estimate the time scale for allosteric switching, which shows that this riboswitch is under kinetic control lending additional support to the conclusion based on single molecule pulling experiments. A consequence of the stability hypothesis is that a single point mutation (U28C) in the P2 helix of the add A-riboswitch, which increases the stability of P2, would make the folding landscapes of the two riboswitches similar. This prediction can be tested in single molecule pulling experiments.
RNA-folding  biophysics  simulation  contingency  energy-landscapes  molecular-design  interesting  nudge-targets  consider:explanatory-model-refinement  note:self-organizing-polymer-model 
march 2014 by Vaguery
[1310.3000] Fractionalization of Interstitials in Curved Colloidal Crystals
Understanding the out-of equilibrium behaviour of point defects in crystals, yields insights into the nature and fragility of the ordered state, as well as being of great practical importance. In some rare cases defects are spontaneously healed - a one-dimensional crystal formed by a line of identical charged particles, for example, can accommodate an interstitial (extra particle) by a re-adjusting all particle positions to even out the spacing. In sharp contrast, particles organized into a perfect hexagonal crystal in the plane cannot accommodate an interstitial by a simple re-adjustment of the particle spacing - the interstitial remains instead trapped between lattice sites and diffuses by hopping, leaving the crystal permanently defected. Here we report on the behavior of interstitials in colloidal crystals on curved surfaces. Using optical tweezers operated independently of three dimensional imaging, we insert a colloidal interstitial in a lattice of similar particles on flat and curved (positively and negatively) oil-glycerol interfaces and image the ensuing dynamics. We find that, unlike in flat space, the curved crystals self-heal through a collective rearrangement that re-distributes the increased density associated with the interstitial. The self-healing process can be interpreted in terms of an out of equilibrium interaction of topological defects with each other and with the underlying curvature. Our observations suggest the existence of "particle fractionalization" on curved surface crystals.
nanotechnology  materials-science  experiment  molecular-design  interesting  outside-the-box 
january 2014 by Vaguery
[1310.4309] Optimizing water permeability through the hourglass shape of aquaporins
The ubiquitous aquaporin channels are able to conduct water across cell membranes, combining the seemingly antagonist functions of a very high selectivity with a remarkable permeability. Whereas molecular details are obvious keys to perform these tasks, the overall efficiency of transport in such nanopores is also strongly limited by viscous dissipation arising at the connection between the nanoconstriction and the nearby bulk reservoirs. In this contribution, we focus on these so-called entrance effects and specifically examine whether the characteristic hourglass shape of aquaporins may arise from a geometrical optimum for such hydrodynamic dissipation. Using a combination of finite-element calculations and analytical modeling, we show that conical entrances with suitable opening angle can indeed provide a large increase of the overall channel permeability. Moreover, the optimal opening angles that maximize the permeability are found to compare well with the angles measured in a large variety of aquaporins. This suggests that the hourglass shape of aquaporins could be the result of a natural selection process toward optimal hydrodynamic transport. Finally, in a biomimetic perspective, these results provide guidelines to design artificial nanopores with optimal performances.
molecular-design  molecular-machinery  biological-engineering  structural-biology  engineering-design 
december 2013 by Vaguery
[1309.6449] Exploring Programmable Self-Assembly in Non-DNA based Molecular Computing
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among them is crucial for controlling the manufacture of desired complex structures at the molecular and supramolecular scale. This work focuses on a programmability model for non DNA-based molecules and complex behaviour analysis of their self-assembled conformations. In particular, we look into modelling, programming and simulation of porphyrin molecules self-assembly and apply Kolgomorov complexity-based techniques to classify and assess simulation results in terms of information content. The analysis focuses on phase transition, clustering, variability and parameter discovery which as a whole pave the way to the notion of complex systems programmability.
self-assembly  nanotechnology  molecular-design  molecular-machinery  stamp-collecting  classification  emergent-design 
november 2013 by Vaguery
[1309.0294] Bottom-up Engineering of Diamond Nanostructures
Engineering nanostructures from the bottom up enables the creation of carefully engineered complex structures that are not accessible via top down fabrication techniques, in particular, complex periodic structures for applications in photonics and sensing. In this work, we propose and demonstrate a bottom up approach that can be adopted and utilized to controllably build diamond nanostructures. A realization of periodic structures and optical wave-guiding is achieved by growing nanoscale single crystal diamond through a defined pattern.
nanotechnology  engineering-design  emergent-design  molecular-design 
september 2013 by Vaguery
[1304.1740] Contact processes in crowded environments
Periodically sheared colloids at low densities demonstrate a dynamical phase transition from an inactive to active phase as the strain amplitude is increased. The inactive phase consists of no collisions/contacts between particles in the steady state limit, while in the active phase collisions persist. To investigate this system at higher densities, we construct and study a conserved-particle-number contact process with novel three-body interactions, which are potentially more likely than two-body interactions at higher densities. For example, consider one active (diffusing) particle colliding with two inactive (non-diffusing) particles such that they become active, in addition to spontaneous inactivation. In mean-field, this system exhibits a continuous dynamical phase transition belonging to the conserved directed percolation universality class. Simulations on square lattices support the mean field result. In contrast, the three-body interaction requiring two active particles to activate one inactive particle exhibits a discontinuous transition. Finally, inspired by kinetically-constrained models of the glass transition, we investigate the "caging effect" at even higher particle densities to look for a second dynamical phase transition back to an inactive phase. Square lattice simulations suggest a continuous transition with a new set of exponents differing from conserved directed percolation, i.e. a new universality class for contact processes with conserved particle number.
simulation  molecular-design  nudge-targets  fluid-dynamics  diffusion  biophysics 
april 2013 by Vaguery
[1302.1853] Cooperative effects enhance the transport properties of molecular spider teams
Molecular spiders are synthetic molecular motors based on DNA nanotechnology. While natural molecular motors have evolved towards very high efficiency, it remains a major challenge to develop efficient designs for man-made molecular motors. Inspired by biological motor proteins like kinesin and myosin, molecular spiders comprise a body and several legs. The legs walk on a lattice that is coated with substrate which can be cleaved catalytically. We propose a novel molecular spider design in which n spiders form a team. Our theoretical considerations show that coupling several spiders together alters the dynamics of the resulting team significantly. Although spiders operate at a scale where diffusion is dominant, spider teams can be tuned to behave nearly ballistic, which results in fast and predictable motion. Based on the separation of time scales of substrate and product dwell times, we develop a theory which utilises equivalence classes to coarse-grain the micro-state space. In addition, we calculate diffusion coefficients of the spider teams, employing a mapping of an n-spider team to an n-dimensional random walker on a confined lattice. We validate these results with Monte Carlo simulations and predict optimal parameters of the molecular spider team architecture which makes their motion most directed and maximally predictable.
nanotechnology  molecular-design  molecular-machinery  molecular-spider-team-ACTIVATE 
april 2013 by Vaguery
[1304.2054] Monte-Carlo Simulation of a Multi-Dimensional Switch-Like Model of Stem Cell Differentiation
The process controlling the diferentiation of stem, or progenitor, cells into one specific functional direction is called lineage specification. An important characteristic of this process is the multi-lineage priming, which requires the simultaneous expression of lineage-specific genes. Prior to commitment to a certain lineage, it has been observed that these genes exhibit intermediate values of their expression levels. Multi-lineage differentiation has been reported for various progenitor cells, and it has been explained through the bifurcation of a metastable state. During the differentiation process the dynamics of the core regulatory network follows a bifurcation, where the metastable state, corresponding to the progenitor cell, is destabilized and the system is forced to choose between the possible developmental alternatives. While this approach gives a reasonable interpretation of the cell fate decision process, it fails to explain the multi-lineage priming characteristic. Here, we describe a new multi-dimensional switch-like model that captures both the process of cell fate decision and the phenomenon of multi-lineage priming. We show that in the symmetrical interaction case, the system exhibits a new type of degenerate bifurcation, characterized by a critical hyperplane, containing an infinite number of critical steady states. This critical hyperplane may be interpreted as the support for the multi-lineage priming states of the progenitor. Also, the cell fate decision (the multi-stability and switching behavior) can be explained by a symmetry breaking in the parameter space of this critical hyperplane. These analytical results are confirmed by Monte-Carlo simulations of the corresponding chemical master equations.
theoretical-biology  systems-biology  developmental-biology  engineering-design  control-theory  molecular-design  nudge-targets  simulation 
april 2013 by Vaguery
[1303.3898] Crumpled globule possesses the properties of molecular machines
Folding and unfolding of a crumpled polymer globule is regarded as a cascade of equilibrium phase transitions in a hierarchical system, similar to the Dyson hierarchical spin model. Studying the relaxation properties of the elastic network of contacts in a crumpled globule, we show that the dynamic properties of hierarchically folded polymer chains in globular phase are similar to those of molecular machines.
molecular-design  molecular-machinery  structural-biology  energy-landscapes  protein-folding  nudge-targets 
march 2013 by Vaguery
[1302.1385] Graphene as a Prototype Crystalline Membrane
The understanding of the structural and thermal properties of membranes, low-dimensional flexible systems in a space of higher dimension, is pursued in many fields from string theory to chemistry and biology. The case of a two-dimensional (2D) membrane in three dimensions is the relevant one for dealing with real materials. Traditionally, membranes are primarily discussed in the context of biological membranes and soft matter in general. The complexity of these systems hindered a realistic description of their interatomic structures based on a truly microscopic approach. Therefore, theories of membranes were developed mostly within phenomenological models. From the point of view of statistical mechanics, membranes at finite temperature are systems governed by interacting long-range fluctuations. Graphene, the first truly two-dimensional system consisting of just one layer of carbon atoms, provides a model system for the development of a microscopic description of membranes. In this Account, we review key results in the microscopic theory of structural and thermal properties of graphene and compare them with the predictions of phenomenological theories. The two approaches are in good agreement for the various scaling properties of correlation functions of atomic displacements. However, some other properties, such as the temperature dependence of the bending rigidity, cannot be understood based on phenomenological approaches. We also consider graphene at very high temperature and compare the results with existing models for two-dimensional melting. The melting of graphene presents a different scenario, and we describe that process as the decomposition of the graphene layer into entangled carbon chains.
chemistry  molecular-design  grapheme  dynamical-systems  structure-function-relationships  biophysics 
march 2013 by Vaguery
[1211.0662] Hidden Complexity in the Isomerization Dynamics of Holliday Junctions
A plausible consequence of rugged energy landscapes of biomolecules is that functionally competent folded states may not be unique, as is generally assumed. Indeed, molecule-to-molecule variations in the dynamics of enzymes and ribozymes under folding conditions have recently been identified in single molecule experiments. However, systematic quantification and the structural origin of the observed complex behavior remain elusive. Even for a relatively simple case of isomerization dynamics in Holliday Junctions (HJs), molecular heterogeneities persist over a long observation time (Tobs ~ 40 sec). Here, using concepts in glass physics and complementary clustering analysis, we provide a quantitative method to analyze the smFRET data probing the isomerization in HJ dynamics. We show that ergodicity of HJ dynamics is effectively broken; as a result, the conformational space of HJs is partitioned into a folding network of kinetically disconnected clusters. While isomerization dynamics in each cluster occurs rapidly as if the associated conformational space is fully sampled, distinct patterns of time series belonging to different clusters do not interconvert on Tobs. Theory suggests that persistent heterogeneity of HJ dynamics is a consequence of internal multiloops with varying sizes and flexibilities frozen by Mg2+ ions. An annealing experiment using Mg2+ pulse that changes the Mg2+ cocentration from high to low to high values lends support to this idea by explicitly showing that interconversions can be driven among trajectories with different patterns.
molecular-design  molecular-machinery  biochemistry  experiment  protein-folding  structural-biology 
march 2013 by Vaguery
[1109.5389] Water drives peptide conformational transitions
"Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that water is the main driving force of the conformational changes."
molecular-design  systems-biology  simulation  intracellular-dynamics  kinda-knew-this-a-long-time-ago  biochemistry 
october 2011 by Vaguery
[1102.2359] A Phyllotactic Approach to the Structure of Collagen Fibrils
"… We examine here how the algorithm of phyllotaxis could contribute to the analysis of the structure of collagen fibrils. Such an algorithm indeed leads to organizations giving to each element of the assembly the most homogeneous and isotropic dense environment in a situation of cylindrical symmetry. The scattered intensity expected from a phyllotactic distribution of triple helices in collagen fibrils well agrees with the major features observed along the equatorial direction of their X ray patterns. Following this approach, the aggregation of triple helices in fibrils should be considered within the frame of soft condensed matter studies rather than that of molecular crystal studies."
self-assembly  nanotechnology  molecular-design  molecular-machinery  theoretical-biology  structural-biology  crystallography  condensed-matter  from delicious
april 2011 by Vaguery
[1008.1101] Control of pathways and yields of protein crystallization through the interplay of nonspecific and specific attractions
"We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths of these interactions. When the nonspecific interaction is strong, liquidlike clustering can precede crystallization; when it is weak, growth can proceed via ordered nuclei. Crystal yields are in certain parameter regimes enhanced by the nonspecific interaction, even though it promotes association without local crystalline order. Our results suggest that equipping nanoscale components with weak nonspecific interactions (such as depletion attractions) can alter both their dynamical pathway of assembly and optimize the yield of the resulting material."
molecular-design  molecular-machinery  simulation  self-assembly  emergent-design  nudge-targets  physics-is-fun 
august 2010 by Vaguery
[0901.1849] Randomized Self-Assembly for Exact Shapes
"Working in Winfree's abstract tile assembly model, we show that a constant-size tile assembly system can be programmed through relative tile concentrations to build an n x n square with high probability, for any sufficiently large n. This answers an open question of Kao and Schweller (Randomized Self-Assembly for Approximate Shapes, ICALP 2008), who showed how to build an approximately n x n square using tile concentration programming, and asked whether the approximation could be made exact with high probability. We show how this technique can be modified to answer another question of Kao and Schweller, by showing that a constant-size tile assembly system can be programmed through tile concentrations to assemble arbitrary finite *scaled shapes*, which are shapes modified by replacing each point with a c x c block of points, for some integer c. …"
molecular-design  nanotechnology  DNA-computing  nudge-targets  emergent-design 
august 2010 by Vaguery
[1003.1324] Passive swimming in low Reynolds number flows
"The possibility of microscopic swimming by extraction of energy from an external flow is discussed, focusing on the migration of a simple trimer across a linear shear flow. The geometric properties of swimming, together with the possible generalization to the case of a vesicle, are analyzed.The mechanism of energy extraction from the flow appears to be the generalization to a discrete swimmer of the tank-treading regime of a vesicle. The swimmer takes advantage of the external flow by both extracting energy for swimming and "sailing" through it. The migration velocity is found to scale linearly in the stroke amplitude, and not quadratically as in a quiescent fluid. This effect turns out to be connected with the non-applicability of the scallop theorem in the presence of external flow fields."
molecular-design  molecular-machinery  biomechanics  nudge-targets  emergent-design 
august 2010 by Vaguery
[1007.3554] Designer disordered materials with large complete photonic band gaps
"We present designs of 2D isotropic, disordered photonic materials of arbitrary size with complete band gaps blocking all directions and polarizations. The designs with the largest gaps are obtained by a constrained optimization method that starts from a hyperuniform disordered point pattern, an array of points whose number variance within a spherical sampling window grows more slowly than the volume. We argue that hyperuniformity, combined with uniform local topology and short-range geometric order, can explain how complete photonic band gaps are possible without long-range translational order. We note the ramifications for electronic and phononic band gaps in disordered materials."
engineering-design  molecular-design  simulation  nudge-targets  photonics  materials-science 
july 2010 by Vaguery
[0902.3631] Distributed Agreement in Tile Self-Assembly
"Laboratory investigations have shown that a formal theory of fault-tolerance will be essential to harness nanoscale self-assembly as a medium of computation. Several researchers have voiced an intuition that self-assembly phenomena are related to the field of distributed computing. This paper formalizes some of that intuition. We construct tile assembly systems that are able to simulate the solution of the wait-free consensus problem in some distributed systems. (For potential future work, this may allow binding errors in tile assembly to be analyzed, and managed, with positive results in distributed computing, as a "blockage" in our tile assembly model is analogous to a crash failure in a distributed computing model.) …We show that solution of this strengthened consensus problem can be simulated by a two-dimensional tile assembly model only for two processes, whereas a three-dimensional tile assembly model can simulate its solution in a distributed system with any number of processes
nanotechnology  self-assembly  molecular-design  distributed-processing  complexology  emergent-design  nudge-targets 
july 2010 by Vaguery
[1007.3712] Formal Verification of Self-Assembling Systems
"This paper introduces the theory and practice of formal verification of self-assembling systems. We interpret a well-studied abstraction of nanomolecular self assembly, the Abstract Tile Assembly Model (aTAM), into Computation Tree Logic (CTL), a temporal logic often used in model checking. We then consider the class of "rectilinear" tile assembly systems. This class includes most aTAM systems studied in the theoretical literature, and all (algorithmic) DNA tile self-assembling systems that have been realized in laboratories to date. We present a polynomial-time algorithm that, given a tile assembly system T as input, either provides a counterexample to T's rectilinearity or verifies whether T has a unique terminal assembly. …"
self-assembly  nanotechnology  emergent-design  molecular-design  molecular-machinery  engineering-design  testing 
july 2010 by Vaguery
PLoS ONE: Is Thermosensing Property of RNA Thermometers Unique?
"… We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at various temperatures using the RNA folding software Vienna. In this study, we compared the thermosensing property of 100 randomly selected mRNAs and three well known thermometers…"
molecular-design  simulation  computational-methods  RNA-folding  biomolecules  nudge-targets  via:twitter 
july 2010 by Vaguery
[1006.4265] Modeling capsid self-assembly: Design and analysis
"A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible, and an explicit solvent is optionally included. …Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered."
molecular-design  virus  biochemistry  self-assembly  simulation  nudge-targets  theoretical-biology  biological-engineering 
june 2010 by Vaguery
[1006.3736] Force-detected nuclear magnetic resonance: Recent advances and future challenges
"We review recent efforts to detect small numbers of nuclear spins using magnetic resonance force microscopy.…"
nanotechnology  atomic-force-microscopy  physics  molecular-design 
june 2010 by Vaguery
[1006.3518] Graphene: A sub-nanometer trans-electrode membrane
"Isolated, atomically thin conducting membranes of graphite, called graphene, have recently been the subject of intense research with the hope that practical applications in fields ranging from electronics to energy science will emerge. Here, we show that when immersed in ionic solution, a layer of graphene takes on new electrochemical properties that make it a trans-electrode. The trans-electrode's properties are the consequence of the atomic scale proximity of its two opposing liquid-solid interfaces together with graphene's well known in-plane conductivity. We show that several trans-electrode properties are revealed by ionic conductivity measurements on a CVD grown graphene membrane that separates two aqueous ionic solutions. Despite this membrane being only one to two atomic layers thick, we find it is a remarkable ionic insulator with a very small stable conductivity that depends on the ion species in solution.…"
nanotechnology  molecular-design  graphene  engineering 
june 2010 by Vaguery
[1002.4273] Mutual information in time-varying biochemical systems
ME: what would 'well-designed' biochemical nets look like, if you evolved them in silico?

"The reliability with which a network can transmit a particular frequency component of the input signal tra- jectory is determined by the gain-to-noise ratio of the net- work as a function of frequency. For systems that obey the spectral addition rule [32], that is those for which downstream reactions do not affect the input signal, the gain-to-noise ratio is an intrinsic property of the processing network. For networks that do not obey the spectral addition rule the gain-to-noise ratio will be dependent on the statistics of the input signal. The mutual information between input and output signals, which quantifies the information which can be transmitted about a particular input ensemble, also depends on the particular choice of the input signal.…"
biochemistry  theoretical-biology  molecular-design  biological-engineering  network-theory  complexology  nudge-targets 
june 2010 by Vaguery
[0912.0027] Temperature 1 Self-Assembly: Deterministic Assembly in 3D and Probabilistic Assembly in 2D
"… In contrast, we show that temperature 1 self-assembly in 3 dimensions, even when growth is restricted to at most 1 step into the third dimension, is capable of simulating a large class of temperature 2 systems, in turn permitting the simulation of arbitrary Turing machines and the assembly of $n\times n$ squares in near optimal $O(\log n)$ tile complexity. Further, we consider temperature 1 probabilistic assembly in 2D, and show that with a logarithmic scale up of tile complexity and shape scale, the same general class of temperature $\tau=2$ systems can be simulated with high probability, yielding Turing machine simulation and $O(\log^2 n)$ assembly of $n\times n$ squares with high probability. Our results show a sharp contrast in achievable tile complexity at temperature 1 if either growth into the third dimension or a small probability of error are permitted. …"
molecular-design  DNA-computing  Wang-tiles  emergent-design  LaBean  nudge-targets 
may 2010 by Vaguery
Untangling the Quantum Entanglement Behind Photosynthesis: Berkeley scientists shine new light on green plant secrets « Berkeley Lab News Center
"The results of this study hold implications not only for the development of artificial photosynthesis systems as a renewable non-polluting source of electrical energy, but also for the future development of quantum-based technologies in areas such as computing – a quantum computer could perform certain operations thousands of times faster than any conventional computer."
photosynthesis  biochemistry  biophysics  molecular-design  quantum-computing  nanotechnology  entanglement 
may 2010 by Vaguery
[1004.4383] Self-Assembly of Arbitrary Shapes with RNA and DNA tiles (extended abstract)
"Staged self-assembly with RNA removal is a model of tile-based algorithmic self-assembly that was introduced by Abel, Benbernou, Damian, Demaine, Demaine, Flatland, Kominers and Schweller (Shape Replication through Self-Assembly and RNase Enzymes, SODA 2010) and is a model that allows for the periodic removal of all tiles in a given assembly that belong to a specially designated group of (RNA) tiles. In this paper, we study the self-assembly of arbitrary shapes in staged assembly systems with RNA removal. We analyze the performance of our assembly systems with respect to their tile complexity, stage complexity as well as the scale factor, connectivity and addressability of the uniquely produced final assembly."
molecular-design  nanotechnology  DNA  biological-engineering 
april 2010 by Vaguery
Sequenomics
Thom LaBean and Erik Schultes start a science thing the three of us know lots about: directed combinatorial molecular design. Looking forward to seeing how they monetize expertise.
startups  Thom-LaBean  Erik-Schultes  sequenomics  science  molecular-design  combinatorial-libraries  biopolymers  bioinformatics  irrational-design 
july 2007 by Vaguery

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