Related papers: Simulating Genomes and Populations in the Mutation…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
The adaptation of biological species to their environment depends on their traits. When various biological processes occur (survival, reproduction, migration, etc.), the trait distribution may change with respect to time and space. In the…
We consider a stochastic individual-based model for the evolution of a haploid, asexually reproducing population. The space of possible traits is given by the vertices of a (possibly directed) finite graph $G=(V,E)$. The evolution of the…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
Mutation testing was proposed to identify weaknesses in test suites by repeatedly generating artificially faulty versions of the software (mutants) and determining if the test suite is sufficient to detect them (kill them). When the tests…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
The time evolution of a simple model for crossover is discussed. A variant of this model with an improved exploration behavior in phase space is derived as a subset of standard one- and multi-point crossover operations. This model is solved…
We propose an effective and flexible scheme for reverse engineering of a Hamiltonian by designing the evolution operators to eliminate the terms of Hamiltonian which are hard to be realized in practice. Different from transitionless quantum…
In social situations with which evolutionary game is concerned, individuals are considered to be heterogeneous in various aspects. In particular, they may differently perceive the same outcome of the game owing to heterogeneity in…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Drug gradients are believed to play an important role in the evolution of bacteria resistant to antibiotics and tumors resistant to anti-cancer drugs. We use a statistical physics model to study the evolution of a population of malignant…
We introduce a method for approximating posterior probabilities of phylogenetic trees and reconstructing ancestral sequences under models of sequence evolution with site-dependence, where standard phylogenetic likelihood computations…
Cancer progression and monotonic accumulation models were developed to discover dependencies in the irreversible acquisition of binary traits from cross-sectional data. They have been used in computational oncology and virology but also in…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
Two important problems affect the ability of asexual populations to accumulate beneficial mutations, and hence to adapt. First, clonal interference causes some beneficial mutations to be outcompeted by more-fit mutations which occur in the…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…
Imitation learning is a popular paradigm to teach robots new tasks, but collecting robot demonstrations through teleoperation or kinesthetic teaching is tedious and time-consuming. In contrast, directly demonstrating a task using our human…
A central challenge in Human Immunodeficiency Virus (HIV) public health policy lies in determining whether to universally expand treatment access, despite the risk of sub-optimal adherence and consequent drug resistance, or to adopt a more…
Adaptation often involves the acquisition of a large number of genomic changes which arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for…