Search results for "dynamics"
showing 10 items of 9782 documents
Modeling of biomolecular machines in non-equilibrium steady states
2021
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate. Equilibrium statistical mechanics guides both the development of models and numerical methods for dynamics obeying detailed balance. For systems driven away from thermal equilibrium such a universal theoretical framework is missing. For a restricted class of driven systems governed by Markov dynamics and local detailed balance, stochastic thermodynamics has evolved to fill this gap and to provide fundamental constraints and guiding principles. The next step…
Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability
2021
Switching between different levels of resolution is essential for multiscale modeling, but restoring details at higher resolution remains challenging. In our previous study we have introduced deepBackmap: a deep neural-network-based approach to reverse-map equilibrated molecular structures for condensed-phase systems. Our method combines data-driven and physics-based aspects, leading to high-quality reconstructed structures. In this work, we expand the scope of our model and examine its chemical transferability. To this end, we train deepBackmap solely on homogeneous molecular liquids of small molecules, and apply it to a more challenging polymer melt. We augment the generator's objective w…
Sharp and fast: sensors and switches based on polymer brushes with adsorption-active minority chains.
2014
We propose a design for polymer-based sensors and switches with sharp switching transition and fast response time. The switching mechanism involves a radical change in the conformations of adsorption-active minority chains in a brush. Such transitions can be induced by a temperature change of only about ten degrees, and the characteristic time of the conformational change is less than a second. We present an analytical theory for these switches and support it by self-consistent field calculations and Brownian dynamics simulations.
Computer simulation of bottle-brush polymers with flexible backbone: good solvent versus theta solvent conditions.
2011
By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\sigma$ side chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range $5 \le N \le 40$, backbone chain lengths are in the range $50 \le N_b \le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, $N_b \le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of …
Charged supramolecular assemblies of surfactant molecules in gas phase
2015
The aim of this review is to critically analyze recent literature on charged supramolecular assemblies formed by surfactant molecules in gas phase. Apart our specific interest on this research area, the stimuli to undertake the task arise from the widespread theoretical and applicative benefits emerging from a comprehensive view of this topic. In fact, the study of the formation, stability, and physicochemical peculiarities of non-covalent assemblies of surfactant molecules in gas phase allows to unveil interesting aspects such as the role of attractive, repulsive, and steric intermolecular interactions as driving force of supramolecular organization in absence of interactions with surround…
Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase
2015
Enzymes are the catalysts used by living organisms to accelerate chemical processes under physiological conditions. In this chapter, we illustrate the current view about the origin of their extraordinary rate enhancement based on molecular simulations and, in particular, on methods based on the combination of Quantum Mechanics and Molecular Mechanics potentials which provide a solution to treat the chemical reactivity of these large and complex molecular systems. Computational studies on Dihydrofolate Reductase have been selected as a conductor wire to present the evolution and difficulties to model chemical reactivity in enzymes. The results discussed here show that experimental observatio…
Giant Mechanocaloric Effects in Fluorite-Structured Superionic Materials
2016
Mechanocaloric materials experience a change in temperature when a mechanical stress is applied on them adiabatically. Thus, far, only ferroelectrics and superelastic metallic alloys have been considered as potential mechanocaloric compounds to be exploited in solid-state cooling applications. Here we show that giant mechanocaloric effects occur in hitherto overlooked fast ion conductors (FIC), a class of multicomponent materials in which above a critical temperature, Ts, a constituent ionic species undergoes a sudden increase in mobility. Using first-principles and molecular dynamics simulations, we found that the superionic transition in fluorite-structured FIC, which is characterized by …
Exploiting seeding of random number generators for efficient domain decomposition parallelization of dissipative particle dynamics
2013
Abstract Dissipative particle dynamics (DPD) is a new promising method commonly used in coarse-grained simulations of soft matter and biomolecular systems at constant temperature. The DPD thermostat involves the evaluation of stochastic or random forces between pairs of neighboring particles in every time step. In a parallel computing environment, the transfer of these forces from node to node can be very time consuming. In this paper we describe the implementation of a seeded random number generator with three input seeds at each step which enables the complete generation of the pairwise stochastic forces in parallel DPD simulations with minimal communication between nodes.
Short hydrogen bonds enhance nonaromatic protein-related fluorescence
2021
Significance Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.
Visualizing Solubilization by a Realistic Particle Model in Chemistry Education
2019
An application for the visualization of the mixing process of two different types of structureless interacting particles is presented. The application allows to demonstrate on a qualitative basis, as well as by quantitatively monitoring the time evolution of the fractions of aggregates of different sizes, that the formation of a homogeneous mixture is the result of favorable solute-solvent interactions as well as by temperature. It is suggested that, along with the use of suitable macroscopic examples, visualizations by the present application are useful in elucidating concepts related to miscibility/solubility. The application is based on a two-dimensional realistic dynamic model where ato…