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Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
Morphogenesis involves the transformation of initially simple shapes, such as multicellular spheroids, into more complex $3D$ shapes. These shape changes are governed by mechanical forces including molecular motor-generated forces as well…
Large-scale deep learning models are well-suited for compression. Across a variety of tasks, methods like pruning, quantization, and knowledge distillation have been used to achieve massive reductions in model parameters with only marginal…
Bone remodeling involves the coordinated removal of bone by osteoclasts and addition of bone by osteoblasts, a process that is modulated by the prevailing mechanical environment. In this paper a fully coupled model of bone remodeling is…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
The ever-increasing parameter counts of deep learning models necessitate effective compression techniques for deployment on resource-constrained devices. This paper explores the application of information geometry, the study of…
Techniques for simulating molecules whose conformations satisfy constraints are presented. A method for selecting appropriate moves in Monte Carlo simulations is given. The resulting moves not only obey the constraints but also maintain…
Electropermeabilization is a clinical technique in cancer treatment to locally stimulate the cell metabolism. It is based on electrical fields that change the properties of the cell membrane. With that, cancer treatment can reach the cell…
We propose a two-scale model to resolve essential features of developmental tissue deformations. The model couples individual cellular behavior to the mechanics at tissue scale. This is realized by a multiphase-field model addressing the…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
A methodology grounded in model reduction is presented for accelerating the gradient-based solution of a family of linear or nonlinear constrained optimization problems where the constraints include at least one linear Partial Differential…
We develop an optimization-based algorithm for parametric model order reduction (PMOR) of linear time-invariant dynamical systems. Our method aims at minimizing the $\mathcal{H}_\infty \otimes \mathcal{L}_\infty$ approximation error in the…
We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Determining the proper level of details to develop and solve physical models is usually difficult when one encounters new engineering problems. Such difficulty comes from how to balance the time (simulation cost) and accuracy for the…
This paper proposes a novel orthogonal-by-construction parametrization for augmenting physics-based input-output models with a learning component in an additive sense. The parametrization allows to jointly optimize the parameters of the…
Ordinary differential equations (ODEs) are widely used to model biological, (bio-)chemical and technical processes. The parameters of these ODEs are often estimated from experimental data using ODE-constrained optimisation. This article…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…