Related papers: Molecular Dynamics Simulation of Amyloid Beta Dime…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Polymers-macromolecular systems composed of repeating chemical units-constitute the molecular foundation of living organisms, while their synthetic counterparts drive transformative advances across medicine, consumer products, and energy…
In a system of atoms with large positive scattering length, weakly-bound diatomic molecules (dimers) are generated dynamically by the strong interactions between the atoms. If the atoms are modeled by a quantum field theory with an atom…
Collections of interacting, self-propelled particles have been extensively studied as minimal models of many living and synthetic systems from bird flocks to active colloids. However, the influence of active rotations in the absence of…
The vibrational dynamics of a model polymer glass is studied by Molecular Dynamics simulations. The focus is on the "soft" monomers with high participation to the lower-frequency vibrational modes contributing to the thermodynamic anomalies…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
We investigate the quantum many-body dynamics of dissociation of a Bose-Einstein condensate of molecular dimers into pairs of constituent bosonic atoms and analyze the resulting atom-atom correlations. The quantum fields of both the…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
Protein amyloid fibrils are a form of linear protein aggregates that are implicated in many neurodegenerative diseases. Here, we study the dynamics of amyloid fibril elongation by performing Langevin dynamic simulations on a coarse-grained…
We observe the low-lying excitations of a molecular dimer formed by two electrons in a GaAs semiconductor quantum dot in which the number of confined electrons is tuned by optical illumination. By employing inelastic light scattering we…
We present results for a lattice model of bio-polymers where the type of $\beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these…
The specific heat is a central property of condensed matter systems including polymers and oligomers in their condensed phases. Yet, predictions of this quantity from molecular simulations and successful comparisons to experimental data are…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…
The competition between evolution time, interaction strength, and temperature challenges our understanding of many-body quantum systems out-of-equilibrium. Here we consider a benchmark system, the Hubbard dimer, which allows us to explore…
Short peptides with antimicrobial activity have therapeutic potential for treating bacterial infections. Mechanisms of actions for antimicrobial peptides require binding the biological membrane of their target, which often represents a key…
We investigate thermal fluctuations in a smectic A phase of an amphiphile-solvent mixture with molecular dynamics simulations. We use an idealized model system, where solvent particles are represented by simple beads, and amphiphiles by…
In this progress report we present a new approach to the ab-initio guided bottom up design of beta-Ti alloys for biomedical applications using a quantum mechanical simulation method in conjunction with experiments. Parameter-free density…
Natively unstructured proteins defy the classical "one sequence-one structure" paradigm of protein science. Monomers of these proteins in pathological conditions can aggregate in the cell, a process that underlies socially relevant…