Related papers: Investigating Biological Matter with Theoretical N…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
A new approach that is a combination of classical thermodynamics and macroscopic kinetics is offered for studying the nucleation kinetics in condensed binary solutions. The theory covers the separation of liquid and solid solutions…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
Life is characterized by a myriad of complex dynamic processes allowing organisms to grow, reproduce, and evolve. Physical approaches for describing systems out of thermodynamic equilibrium have been increasingly applied to living systems,…
We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Ultrafast optical techniques allow to study ultrafast molecular dynamics involving both nuclear and electronic motion.To support interpretation, theoretical approaches are needed that can describe both the nuclear and electron…