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Traditional statistical approaches primarily aim to model associations between variables, but many scientific and practical questions require causal methods instead. These approaches rely on assumptions about an underlying structure, often…
Emergence of collective dynamical chirality (CDC) at mesoscopic scales plays a key role in many formation processes of chiral structures in nature, which may also provide possible routines for people to fabricate complex chiral…
Both ordered and disordered microphases ubiquitously form in suspensions of particles that interact through competing short-range attraction and long-range repulsion (SALR). While ordered microphases are more appealing materials targets,…
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…
Robustness of biochemical systems has become one of the central questions in Systems Biology, although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Despite intense efforts in basic and clinical research, an individualized ventilation strategy for critically ill patients remains a major challenge. Recently, dynamic treatment regime (DTR) with reinforcement learning (RL) on electronic…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
There is an abundance of complex dynamic systems that are critical to our daily lives and our society but that are hardly understood, and even with today's possibilities to sense and collect large amounts of experimental data, they are so…
Classifying chemicals according to putative modes of action (MOAs) is of paramount importance in the context of risk assessment. However, current methods are only able to handle a very small proportion of the existing chemicals. We address…
The rapid evolution of network services demands new paradigms for studying and designing networks. In order to understand the underlying mechanisms that provide network functions, we propose a framework which enables the functional analysis…
Magombedze and Mulder in 2013 studied the gene regulatory system of Mycobacterium Tuberculosis (Mtb) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each subsystem, in the…
With the help of a mathematical model, the metabolic process of the Krebs cycle is studied. The autocatalytic processes resulting in both the formation of the self-organization in the Krebs cycle and the appearance of a cyclicity of its…
Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate…
A prototype for a web application was designed and implemented as a guide to be used by clinicians when designing the best drug therapy for a specific cancer patient, given biological data derived from the patients tumor tissue biopsy. A…
Learning causal relationships between variables is a well-studied problem in statistics, with many important applications in science. However, modeling real-world systems remain challenging, as most existing algorithms assume that the…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
The tailored coupled cluster (TCC) approach is a promising ansatz that preserves the simplicity of single-reference coupled cluster theory, while incorporating a multi-reference wave function through amplitudes obtained from a preceding…
Several researchers have explored the temporal aspect of association rules mining. In this paper, we focus on the cyclic association rules, in order to discover correlations among items characterized by regular cyclic variation overtime.…
As one of the most prevalent diseases worldwide, plaque formation in human arteries, known as atherosclerosis, is the focus of many research efforts. Previously, molecular communication (MC) models have been proposed to capture and analyze…
The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic, steric, electron density…