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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…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Large contingency tables summarizing categorical variables arise in many areas. For example in biology when a large number of biomarkers are cross-tabulated according to their discrete expression level. Interactions of the variables are…
Understanding the development of adolescent behavioral and mental health outcomes requires integrating genetic predisposition, environmental exposures, and neurobiological processes over time. Here, we present a unified quantitative…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
Granular simulations are used to probe the particle scale dynamics at short, intermediate, and long time scales for gravity driven, dense granular flows down an inclined plane. On approach to the angle of repose, where motion ceases, the…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
We use Lagrangian formalism and jet spaces to derive a computational model to simulate multibody dynamics with holonomic constraints. Our approach avoids the traditional problems of drift-off and spurious oscillations. Hence even long…
Hematopoiesis is a complex biological process that leads to the production and regulation of blood cells. It is based upon differentiation of stem cells under the action of growth factors. A mathematical approach of this process is proposed…
It is essential to find new ways of enabling experts in different disciplines to collaborate more efficient in the development of ever more complex systems, under increasing market pressures. One possible solution for this challenge is to…
In this paper, we derive an effective model for transport processes in periodically perforated elastic media, taking into account, e.g., cyclic elastic deformations as they occur in lung tissue due to respiratory movement. The underlying…
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location…
Osmosis plays a central role in the function of living and soft matter systems. While the thermodynamics of osmosis is well understood, the underlying microscopic dynamical mechanisms remain the subject of discussion. Unraveling these…
Biomaterial systems have allowed for the in vitro production of complex, emergent tissue behaviors that were not possible with conventional 2D culture systems allowing for analysis of the normal development as well as disease processes. We…
Operations research practitioners frequently want to model complicated functions that are are difficult to encode in their underlying optimisation framework. A common approach is to solve an approximate model, and to use a simulation to…
Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…