Related papers: Lipid thermodynamics : melting is molecular
Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…
We have adapted a set of classification algorithms, also known as Machine Learning, to the identification of fluid and gel domains close to the main transition of dipalmitoyl-phosphatidylcholine (DPPC) bilayers. Using atomistic molecular…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD) [J. Chem.…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Machine learning techniques including neural networks are popular tools for materials and chemical scientists with applications that may provide viable alternative methods in the analysis of structure and energetics of systems ranging from…
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Consistently atomistic understanding of the mechanism behind the intriguing behavior of low-dimensional systems including monatomic chains, hollow tubes, surface skins, nanocavities, nanowires, and nanograins has long been a high challenge.…
Lipid membranes form the barrier between the inside and outside of cells and many of their subcompartments. As such, they bind to a wide variety of nano- and micrometer sized objects and, in the presence of strong adhesive forces, strongly…
Native membranes of biological cells display melting transitions of their lipids at a temperature of 10-20 degrees below body temperature. Such transitions can be observed in various bacterial cells, in nerves, in cancer cells, but also in…
Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with different types of intrinsic stiffness. Important static observables of the single chain such as gyration radius or persistence length are…
Proteins are vital biological molecules found in every living organism, and their function is determined by what shape they fold into. Peptides are essentially subsets of proteins, and therefore ideal as model systems for protein folding.…
We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
We study a continuum model of the lipid bilayer based on minimizing the free energy of a mixture of water and lipid molecules. This paper extends previous work by Blom & Peletier (2004) in the following ways. (a) It formulates a more…
Conventional molecular dynamics simulation has been used to determine melting temperature of highly compressed classical molecular hydrogen in a wide range of pressures and temperatures using non-empirical atom-atom potentials…