Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment.

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only).

Thermal Gaussian molecular dynamics for quantum dynamics simulations of many-body systems: application to liquid para-hydrogen.

A new method, here called thermal Gaussian molecular dynamics (TGMD), for simulating the dynamics of quantum many-body systems has recently been introduced [I. Georgescu and V. A.

The ground state estimation by global optimization of an effective potential. Application to binary para-H(2)/ortho-D(2) molecular clusters.

It is demonstrated how the problem of ground state estimation of an n-body system can be recast as the less demanding problem of finding the global minimum of an effective potential in the 3n-dimensional coordinate space. The latter emerges when the solution of the imaginary-time Schrödinger equation is approximated by a variational Gaussian wavepacket (VGW). The VGW becomes stationary in the infinite-imaginary-time limit.

Quantum disordering versus melting in Lennard-Jones clusters.

The ground states of Lennard-Jones clusters for sizes up to n=147 are estimated as a function of the de Boer quantum delocalization length Lambda , and the n-Lambda "phase diagram" is constructed. The increase in Lambda favors more disordered and diffuse structures over more symmetric and compact ones, eventually making the liquidlike motif most energetically favorable. The analogy between the quantum- and thermally-induced structural transitions is explored.

Effects of quantum delocalization on structural changes in Lennard-Jones clusters.

The ground states of Lennard-Jones clusters (LJ(n)) for sizes up to n = 147 are estimated as a function of the de Boer quantum delocalization length, Lambda, using the variational Gaussian wavepacket method. Consequently, the n-Lambda phase diagram is constructed showing the ranges of stability of various structural motifs, including the Mackay and anti-Mackay icosahedra, several nonicosahedral but highly symmetric structures, and liquidlike (or disordered) structures. The increase in Lambda favors more disordered and diffuse structures over more symmetric and compact ones, eventually making the liquidlike structures most energetically favorable.

Quantum transitions in Lennard-Jones clusters.

The ground states of Lennard-Jones (LJ) clusters are estimated by finding the Gaussian wave packets that minimize the energy functional. A "phase diagram" for LJ_{n} as a function of size (n=31,..