Search results for "molecular dynamics"
showing 10 items of 1075 documents
Abrupt elastic-to-plastic transition in pentagonal nanowires under bending
2019
MD modeling and calculations were supported by Russian Science Foundation project grant 18-19-00645 “Adhesion of polymer-based soft materials: from liquid to solid”; mechanical testing and FEM simulations were supported by Estonian Research Council projects PUT1689 and PUT1372.
A multi-scale method for complex flows of non-Newtonian fluids
2021
We introduce a new heterogeneous multi-scale method for the simulation of flows of non-Newtonian fluids in general geometries and present its application to paradigmatic two-dimensional flows of polymeric fluids. Our method combines micro-scale data from non-equilibrium molecular dynamics (NEMD) with macro-scale continuum equations to achieve a data-driven prediction of complex flows. At the continuum level, the method is model-free, since the Cauchy stress tensor is determined locally in space and time from NEMD data. The modelling effort is thus limited to the identification of suitable interaction potentials at the micro-scale. Compared to previous proposals, our approach takes into acco…
Flexibility in the Graphene Sheet: The Influence on Gas Adsorption from Molecular Dynamics Studies
2019
Despite being considered completely rigid in most studies, graphene is really flexible leading to out-of-plane movements. In this work, the influence of such flexibility on the adsorption of methane and nitrogen on graphene is studied using molecular dynamics. Indeed, we have used intramolecular force fields for graphene with in-plane and out-of-plane components that allow for describing the movements and deformations of the graphene sheets and providing a more realistic description of the adsorbent. In addition, intermolecular force fields validated at the CCSD(T) level are used. We show that considering the movement of graphene in the adsorption study significantly improves the performanc…
Environmental Noise and Nonlinear Relaxation in Biological Systems
2012
We analyse the effects of environmental noise in three different biological systems: (i) mating behaviour of individuals of 'Nezara viridula' (L.) (Heteroptera Pentatomidae); (ii) polymer translocation in crowded solution; (iii) an ecosystem described by a Verhulst model with a multiplicative Lèvy noise. Specifically, we report on experiments on the behavioural response of 'N. viridula' individuals to sub-threshold deterministic signals in the presence of noise. We analyse the insect response by directionality tests performed on a group of male individuals at different noise intensities. The percentage of insects which react to the sub-threshold signal shows a non-monotonic behavior, charac…
Dielectric Relaxation of a Polybutadiene Melt at a Crystalline Graphite Surface: Atomistic Molecular Dynamics Simulations
2014
Dielectric experiments are an indispensable tool to further our understanding of the relaxation behavior of polymers, not only in bulk samples but also in confined situations. A chemically realistic Molecular Dynamics simulation, in which all information about molecular motions is available, can shed light onto the questions of heterogeneity and anisotropy of the underlying molecular relaxation processes which lead to the ensemble averaged experimental dielectric signal. In this contribution, we present a careful analysis of the dielectric response of a weakly polar and confined polymer, 1,4-polybutadiene between graphite walls. The relaxation of the segmental dipole moments was obtained in…
Frequency-dependent hydrodynamic interaction between two solid spheres
2017
Hydrodynamic interactions play an important role in many areas of soft matter science. In simulations with implicit solvent, various techniques such as Brownian or Stokesian dynamics explicitly include hydrodynamic interactions a posteriori by using hydrodynamic diffusion tensors derived from the Stokes equation. However, this equation assumes the interaction to be instantaneous which is an idealized approximation and only valid on long time scales. In the present paper, we go one step further and analyze the time-dependence of hydrodynamic interactions in a compressible fluid on the basis of the linearized Navier-Stokes equation. The theoretical results show that the compressibility of the…
Ab Initio Phase Diagram of Chromium to 2.5 TPa
2022
Chromium possesses remarkable physical properties such as hardness and corrosion resistance. Chromium is also a very important geophysical material as it is assumed that lighter Cr isotopes were dissolved in the Earth’s molten core during the planet’s formation, which makes Cr one of the main constituents of the Earth’s core. Unfortunately, Cr has remained one of the least studied 3d transition metals. In a very recent combined experimental and theoretical study (Anzellini et al., Scientific Reports, 2022), the equation of state and melting curve of chromium were studied to 150 GPa, and it was determined that the ambient body-centered cubic (bcc) phase of crystalline Cr re…
Physics and biophysics of solvent induced forces: hydrophobic interactions and context-dependent hydration
1998
Solvent induced forces (SIFs) among solutes derive from solvent structural modification due to solutes, and consequent thermodynamic drive towards minimization of related free energy costs. The role of SIFs in biomolecular conformation and function is appreciated by observing that typical SIF values fall within the 20–200 pN interval, and that proteins are stable by only a few kcal mol–1 (1 kcal mol–1 corresponds to 70 pN A). Here we study SIFs, in systems of increasing complexity, using Molecular Dynamics (MD) simulations which give time- and space-resolved details on the biologically significant scale of single protein residues and sidechains. Of particular biological relevance among our …
Simulations and Experiments in Protein Folding
2014
The interplay between simulations and experiments of protein folding has largely contributed to the elucidation of many important aspects of the phenomenon. In this chapter, I briefly describe the experiments which provide information on the kinetics of the protein folding process, and help to characterize the folding transition state. Then, I show how to probe the kinetics of protein folding using molecular dynamics simulations, how to compare the simulations with the experiments and how to help and rationalize the latter, ultimately offering a molecular picture of the process. After the production of suitable molecular dynamics simulation data in the form of trajectories, the procedure in…
Redox potentials and acidity constants from density functional theory based molecular dynamics.
2014
CONSPECTUS: All-atom methods treat solute and solvent at the same level of electronic structure theory and statistical mechanics. All-atom computation of acidity constants (pKa) and redox potentials is still a challenge. In this Account, we review such a method combining density functional theory based molecular dynamics (DFTMD) and free energy perturbation (FEP) methods. The key computational tool is a FEP based method for reversible insertion of a proton or electron in a periodic DFTMD model system. The free energy of insertion (work function) is computed by thermodynamic integration of vertical energy gaps obtained from total energy differences. The problem of the loss of a physical refe…