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Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…
In cheminformatics, network representations of the space of compounds have been suggested extensively. Among these, the threshold-network consists of nodes representing molecules. In this network representation, two molecules are connected…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…
Pauling had proposed that charge is transferred from the more electronegative atom to the less electronegative one during metallic alloying. An expression has recently been derived for the energy of the unlike atom-pair bond using that…
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…
Charge transfer in collisions of Na_n^+ cluster ions with Cs atoms is investigated theoretically in the microscopic framework of non-adiabatic quantum molecular dynamics. The competing reaction channels and related processes affecting the…
Compartmental models based on tracer mass balance are extensively used in clinical and pre-clinical nuclear medicine in order to obtain quantitative information on tracer metabolism in the biological tissue. This paper is the first of a…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
We study a complex formation between the DNA and cationic amphiphilic molecules. As the amphiphile is added to the solution containing DNA, a cooperative binding of surfactants to the DNA molecules is found. This binding transition occurs…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
Exchange couplings are fundamental to our understanding of many physical phenomena in condensed matter physics and material science. Model systems provide a controlled environment to investigate such phenomena, effectively. In this study,…
Calculating intermolecular charge transfer integrals in organic semiconductors requires substantial computer resource for each individual calculation. We might alternatively construct a machine learning model for transfer integrals, which…
Quantifying the effects of amino acid mutations in proteins presents a significant challenge due to the vast combinations of residue sites and amino acid types, making experimental approaches costly and time-consuming. The Potts model has…
We use a numerically exact real-time path integral Monte Carlo scheme to compute electron transfer dynamics between two redox sites within a spin-boson approach. The case of asymmetric reactions is studied in detail in the least understood…