Related papers: A Rational Method for Probing Macromolecules Disso…
The quantum-dynamical mechanism of photoinduced subpicosecond exciton dissociation and the concomitant formation of a charge-separated state at a TFB:F8BT polymer heterojunction is elucidated. The analysis is based upon a two-state vibronic…
We present a systematic hierarchy of approximations for {\it local} exact-decoupling of four-component quantum chemical Hamiltonians based on the Dirac equation. Our ansatz reaches beyond the trivial local approximation that is based on a…
Quantum mechanics of a general one dimensional dissipative system investigated by it's coupling to a Klein-Gordon field as the environment using a minimal coupling method. Heisenberg equation for such a dissipative system containing a…
Electrostatic interactions fundamentally govern the structure, stability, and dynamics of charged (bio)matter, yet the impact of heterogeneous and anisotropic charge distributions on the behavior of protein solutions remains elusive. Here,…
Unfolding, in the context of high-energy particle physics, refers to the process of removing detector distortions in experimental data. The resulting unfolded measurements are straightforward to use for direct comparisons between…
Although atomistic simulations of proteins and other biological systems are approaching microsecond timescales, the quality of trajectories has remained difficult to assess. Such assessment is critical not only for establishing the…
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
We present an in-depth many-body investigation of the so-called mesoscopic molecular ions that can build-up when an ion is immersed into an atomic Bose-Einstein condensate in one dimension. To this end, we employ the Multi-Layer…
Concentrated solutions of monoclonal antibodies have attracted considerable attention due to their importance in pharmaceutical formulations, yet their tendency to aggregate and the resulting high solution viscosity has posed considerable…
The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…
In this paper, we present a splitting algorithm to solve multicomponent transport models. These models are related to plasma simulations, in which we consider the local thermodynamic equilibrium and weakly ionised plasma-mixture models that…
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
One of the fundamental steps toward understanding a complex system is identifying variation at the scale of the system's components that is most relevant to behavior on a macroscopic scale. Mutual information provides a natural means of…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Modeling dispersed solid phases in fluids still represents a computational challenge when considering a small-scale coupling in wide systems, such as the atmosphere or industrial processes at high Reynolds numbers. A numerical method is…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…
A model of postphotodissociative monomolecular (geminate) recombination of heme proteins with small ligands (NO, O2 or CO) is represented. The non-exponential decay with time for the probability to find a heme in unbound state is…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
A 3D Cellular Automaton model developed by the authors to deal with the dynamics of N-body interactions has been adapted to investigate the head-on collision of two identical bound clusters of particles, and the ensuing process of…