Reactions at the water/solid interface are central to development of sustainable processes, from biomass upgrading photo- and electrocatalysis. To gain atomistic insight into these reactions, modeling approaches have been constantly improved over past decade. Polarisable continuum models considerably description charge separation enabled a proper inclusion surface polarization in electrochemist...

A mathematical framework for the coupling of atomistic and continuum models by blending them over a subdomain subject to a constraint is developed. Using the framework, four classes of atomistic-to-continuum (AtC) blending methods are established, their consistency is studied, and their relative merits are discussed. In addition, the framework helps clarify the origin of ghost forces and formal...

Biopolymers such as proteins, DNA and RNA fold into large, macromolecular chiral structures. As charged macromolecules, they absorb strongly in the terahertz due to large-scale collective vibrational modes; as chiral objects, this absorption should be coupled with significant circular dichroism. Terahertz circular dichroism (TCD) is potentially important as a biospecific sensor, unobscured by s...

The H and C Nuclear Magnetic Resonance (NMR) spectra of the retinyl chromophore in rhodopsin are investigated by using Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid methods at the Density Functional Theory (DFT) B3LYP/631G*:Amber level, in conjunction with the Gauge Independent Atomic Orbital (GIAO) method for the ab initio Self-Consistent-Field (SCF) calculation of NMR chemical shifts. ...

We introduce a multiscale framework to simulate inhomogeneous fluids by coarse-graining an all-atom molecular dynamics (MD) trajectory onto sequential snapshots of hydrodynamic fields. We show that the field representation of an atomistic trajectory is quantitatively described by a dynamic field-theoretic model that couples hydrodynamic fluctuations with a Ginzburg-Landau free energy. For liqui...

We have investigated the effect of solvation and confinement on an artificial photosynthetic material, carotenoid-porphyrin-C(60) molecular triad, by a multiscale approach and an enhanced sampling technique. We have developed a combined approach of quantum chemistry, statistical physics, and all-atomistic molecular dynamics simulation to determine the partial atomic charges of the ground-state ...

We investigated the structural and energetic determinants underlying water permeation through peptidic nanopores, motivated by recent experimental findings that indicate that water mobility in single-file water channels displays nonlinear length dependence. To address the molecular mechanism determining the observed length dependence, we studied water permeability in a series of designed gramic...

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods fo...

Chitin and protein are two main building blocks for many natural biomaterials such as crustacean cuticles, sponge skeletons and squid beaks. These biological materials gain growing interests with respect to biomimetic material design, since they possess great mechanical properties due to their evolutionarily refined structures at different hierarchy levels. The interaction between chitin and pr...