Related papers: Multi-site Reaction Dynamics Through Multi-fragmen…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Electronic nearsightedness is one of the fundamental principles governing the behavior of condensed matter and supporting its description in terms of local entities such as chemical bonds. Locality also underlies the tremendous success of…
The study of entanglement in strongly correlated electron systems typically requires knowledge of the reduced density matrix. Here, we apply the parquet dynamical vertex approximation to study the two-site reduced density matrix at varying…
The projection-based quantum embedding method is applied to electronically excited states of valence, Rydberg, and charge-transfer character, valence- and core-ionized states, as well as bound and temporary radical anions. We embed…
Two roads are presently being followed in order to establish the existence of a liquid-gas phase transition in finite nuclear systems from nuclear reactions at high energy. The clean experiment of observing the thermodynamic properties of a…
We present a molecular extension of our recently proposed Green's function embedding method, interacting-bath dynamical embedding theory (ibDET), for computing charged excitation energies at the $GW$ and EOM-CCSD levels. Starting from…
A multiscale theory of interacting continuum mechanics and thermodynamics of mixtures of fluids, electrodynamics, polarization and magnetization is proposed. The mechanical (reversible) part of the theory is constructed in a purely…
A general phenomenological reaction-diffusion model for flow-induced phase transitions in complex fluids is presented. The model consists of an equation of motion for a nonconserved composition variable, coupled to a Newtonian stress…
Polynomial dynamical systems are widely used to model and study real phenomena. In biochemistry, they are the preferred choice for modelling the concentration of chemical species in reaction networks with mass-action kinetics. These systems…
A mesoscopic multi-particle collision model for fluid dynamics is generalized to incorporate the chemical reactions among species that may diffuse at different rates. This generalization provides a means to simulate reaction-diffusion…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used…
Multiple scattering theory is applied to low-energy electron collisions with a complex target formed of two molecular scatterers. The total T-matrix is expressed in terms of the T-matrix for each isolated molecule. We apply the approach to…
Trapping by active sites on surfaces plays important roles in various chemical and biological processes, including catalysis, enzymatic reactions, and viral entry into host cells. However, the mechanisms of these processes remain not well…
The onset of life is often framed around membrane bound compartments and encoded metabolism, leaving unresolved how spatial organization arose before stable boundaries. In this context, environmental gradients are usually treated as…
Density functional theory (DFT), the most widely adopted method in modern computational chemistry, fails to describe accurately the electronic structure of strongly correlated systems. Here we show that DFT can be formally and practically…
Multienzyme cascaded reactions are widely utilized because they can generate value-added biomaterials and biodevices from simple raw materials. However, how to promote the catalytic efficiency and synergistic effect of the multienzyme…
We introduce Extended Density Matrix Embedding Theory (EDMET), a static quantum embedding theory explicitly self-consistent with respect to local two-body physics. This overcomes the biggest practical and conceptual limitation of more…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…