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The cell cycle is tightly regulated by cyclins and their catalytic moieties, the cyclin-dependent kinases (CDKs). Cyclin D1, in association with CDK4/6, acts as a mitogenic sensor and integrates extracellular mitogenic signals and cell…
We review J. Zimanyi's key contributions to the theoretical understanding of dynamical freeze-out in nuclear collisions and their subsequent applications to ultra-relativistic heavy-ion collisions, leading to the discovery of a freeze-out…
The formal structure of geometrical thermodynamics is reviewed with particular emphasis on the geometry of equilibria submanifolds. On these submanifolds thermodynamic metrics are defined as the Hessian of thermodynamic potentials. Links…
We use the formalism of Geometrothermodynamics to describe chemical reactions in the context of equilibrium thermodynamics. Any chemical reaction in a closed system is shown to be described by a geodesic in a $2-$dimensional manifold that…
In this work we study the diffusion mechanisms in lithium disilicate melt using molecular dynamics simulation, which has an edge over other simulation methods because it can track down actual atomic rearrangements in materials once a…
The physicochemical mechanisms underlying the pyrolysis of n-hexane in a high temperature Ar-H2 environment were investigated for plasma pyrolysis process. An optimal chemical kinetics model was developed using the Reaction Mechanism…
The paper gives an account of a detailed investigation of the thermodynamic branch as a path of the chemical system deviation from its isolated thermodynamic equilibrium under an external impact. For a combination of direct and reverse…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
It is shown that kinetic freeze-out in relativistic heavy-ion collisions invariably entails a non-trivial dependence of the freeze-out temperature on the collision centrality. The centrality independence of the chemical freeze-out…
Bio-molecules are active agents in that they consume energy to perform tasks. The standard theoretical description, however, considers only a system-external work agent. Fluctuation theorems, for example, do not allow work-exchange between…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
Many processes of scientific and technological interest are characterized by time scales that render their simulation impossible if one uses present day simulation capabilities. To overcome this challenge a variety of enhanced simulation…
A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a…
The two-body knock-out reaction 4He(e,e'd)d is calculated at various momentum transfers. The full four-nucleon dynamics is taken into account microscopically both in the initial and the final states. As NN interaction the central MT-I/III…
The additive-free tetrazine/enol ether click reaction was performed in ultra-high vacuum (UHV) with an enol ether group covalently linked to a silicon surface: Dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate molecules were coupled to the enol…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
We show that ultracold chemical reactions can be manipulated and controlled by using Rydberg-dressed interactions. Scattering in the ultracold regime is sensitive to long-range interactions, especially when weakly bound (or quasi-bound)…
The rational development of specific inhibitors for the ~500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP…
Reactions on surfaces play an important role in many technological applications. Since these processes are often rather complex, one tries to understand single steps of these complicated reactions by investigating simpler system. In…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…