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Experimental mechanisms that yield the growth of homochiral copolymers over their heterochiral counterparts have been advocated by Lahav and co-workers. These chiral amplification mechanisms proceed through racemic {\beta}-sheet-controlled…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
Revealing relationships between genes and disease phenotypes is a critical problem in biomedical studies. This problem has been challenged by the heterogeneity of diseases. Patients of a perceived same disease may form multiple subgroups,…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…
Spatial organization of chromatin plays a critical role in genome regulation. Various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at…
We investigate Lam\'e systems in periodically perforated domains, and establish quantitative homogenization results in the setting where the domain is clamped at the boundary of the holes. Our method is based on layer potentials and it…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
Lattice mismatch can substantially impact the spatial organization of heterogeneous materials. We examine a simple model for lattice-mismatched solids over a broad range of temperature and composition, revealing both uniform and spatially…
Meta-materials are an important emerging class of engineered materials in which complex macroscopic behaviour--whether electromagnetic, thermal, or mechanical--arises from modular substructure. Simulation and optimization of these materials…
Biological cells are built up from many different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements such as atomic…
The baseline level of transcription, which is variable and difficult to quantify, seriously complicates the normalization of comparative transcriptomic data, but its biological importance remains unappreciated. We show that this currently…
Eumelanin is regarded to be an attractive candidate material for biomedical applications. Despite many theoretical studies exploring the structure of eumelanin, an exact mapping of the energetic landscape of the very large phase space of…
Carcinogenesis is a complex process that involves dynamically inter-connected modular sub-networks that evolve under the influence of micro-environmentally induced perturbations, in non-random, pseudo-Markov chain processes. An appropriate…
In many applications, data can be heterogeneous in the sense of spanning latent groups with different underlying distributions. When predictive models are applied to such data the heterogeneity can affect both predictive performance and…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
In order to grasp the features arising from cellular discreteness and individuality, in large parts of cell tissue modelling agent-based models are favoured. The subclass of off-lattice models allows for a physical motivation of the…
Colour vision has long fascinated scientists, who have sought to understand both the physiology of the mechanics of colour vision and the psychophysics of colour perception. We consider representations of colour in anatomically constrained…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
Hematopoiesis is the process of blood cell formation, through which progenitor stem cells differentiate into mature forms, such as white and red blood cells or mature platelets. While the precursors of the mature forms share many regulatory…