Related papers: A microscopic description of acid-base equilibrium
Ab initio techniques have revolutionised the way in which theory can help practitioners to explore critical mechanisms that govern reactions or properties, and to develop new strategies for materials discovery and design. Yet, their…
In the context of nuclear fuel recycling and environmental issues, the understanding of the properties of radio-elements with various approaches remains a challenge regarding their dangerousness. Moreover, experimentally, it is imperative…
The molecular structure of moving contact lines (MCLs) and the emergence of a corresponding macroscopic dissipation have made the MCL a paradigm of fluid dynamics. Through novel averaging techniques that remove capillary waves smearing we…
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
The rapid advancements in ultrafast laser technology have paved the way for pumping and probing the out-of-equilibrium dynamics of nuclei in crystals. However, interpreting these experiments is extremely challenging due to the complex…
Chemical processes in closed systems are poorly controllable since they always relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…
Despite being a fundamental tool in soft matter research, quartz crystal microbalance (QCM) analyses of discrete macromolecules in liquid so far lack a firm theoretical basis. Currently, acoustic signals are qualitatively interpreted using…