All posts under tag "Quantitative Biology"
Here is suggested a solution to the accommodation-vergence mismatch problem in 3D stereoscopic displays. It can be achieved by compensating the mismatched focal length with refractive power of adjustable-focus 3D glasses. The compensation would make vergence of human eyes match with position of virt
Single-cell data analysis has the potential to revolutionize personalized medicine by characterizing disease-associated molecular changes at the single-cell level. Advanced single-cell multimodal assays can now simultaneously measure various molecules (e.g., DNA, RNA, Protein) across hundreds of tho
In the recent paper of Valleriani {it et al} [Phys. Rev. E {bf 83}, 042903 (2011)], a simple model for describing the translation of messenger RNA (mRNA) by ribosomes is presented, and an expression of the translational ratio $r$, defined as the ratio of translation rate $omega_{rm tl}$ of protein f
We revisit the classical problem of nucleated polymerisation and derive a range of exact results describing polymerisation in systems intermediate between the well-known limiting cases of a reaction starting from purely soluble material and for a reaction where no new growth nuclei are formed.
We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes
Developmental amnesia, featured with severely impaired episodic memory and almost normal semantic memory, has been discovered to occur in children with hippocampal atrophy. This unique combination of characteristics seems to challenge the understanding that early loss of episodic memory may impede c
The puzzle presented by the famous stumps of Gilboa, New York, finds a solution in the discovery of two fossil specimens that allow the entire structure of these early trees to be reconstructed.
Sequences of events in noise-driven excitable systems with slow variables often show serial correlations among their intervals of events. Here, we employ a master equation for general non-renewal processes to calculate the interval and count statistics of superimposed processes governed by a slow ad
Both external environmental selection and internal lower-level evolution are essential for an integral picture of evolution. This paper proposes that the division of internal evolution into DNA/RNA pattern formation (genotype) and protein functional action (phenotype) resolves a universal conflict b
Electroencephalogram, an influential equipment for analyzing humans activities and recognition of seizure attacks can play a crucial role in designing accurate systems which can distinguish ictal seizures from regular brain alertness, since it is the first step towards accomplishing a high accuracy
With the National Toxicology Program issuing its final report on cancer, rats and cell phone radiation, one can draw the following conclusions from their data. There is a roughly linear relationship between gliomas (brain cancers) and schwannomas (cancers of the nerve sheaths around the heart) with
Mental events are considered to supervene on physical events. A supervenient event does not change without a corresponding change in the underlying subvenient physical events. Since wholes and their parts exhibit the same supervenience-subvenience relations, inter-level causation has been expected t
Differential operators can detect significant changes in signals. This has been utilized to enhance the contrast of the seizure signatures in depth EEG or ECoG. We have actually taken normalized exponential of absolute value of single or double derivative of epileptic ECoG. Variance operation has be
Human activity has an enormous impact on Earth, changing organisms, environments and landscapes, leading to the decline of original ecosystems and irreversible changes that create new combinations of living beings and materials. As a result, ecosystems with new properties and new species pools are e
Effect of terahertz radiation (3.6 THz, 81.5 mkm,15 mV) on some behavioral patterns of intact mice has been investigated. In home cage mice demonstrated avoidance of laser ray and enhanced replacement activity in free behavior. Animals irradiated during 30 minutes manifested an increased level of an
Life over the past four billion years has been shaped by proteins and their capacity to assemble into three dimensional conformations. Protein sequence alignments have been the enabling technology for exploring the evolution and functional adaptation of proteins across the tree of life. Recent advan
This paper deals with a model of cellular growth called 'Epigenetic Tracking', whose key features are: i) distinction bewteen 'normal' and 'driver' cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the cell in the driver cell lineage tree and represents the sour
Complex change is often described as 'evolutionary' in economics, policy, and technology, yet most system dynamics models remain constrained to fixed state spaces and equilibrium-seeking behavior. This paper argues that evolutionary dynamics should be treated as a core system-thinking problem rather
Effective representations of protein sequences are widely recognized as a cornerstone of machine learning-based protein design. Yet, protein bioengineering poses unique challenges for sequence representation, as experimental datasets typically feature few mutations, which are either sparsely distrib
Motivation: Antifungal resistance has become an increasing global concern in both clinical and environmental health. Detecting known resistance mutations directly from sequencing reads, in special metagenomic samples, remains a major challenge. As fungal pathogens are often neglected compared with b
In simulations of sexual reproduction with diploid individuals, we introduce that female haploid gametes recognize one specific allele of the genomes as a marker of the male haploid gametes. They fuse to zygotes preferrably with male gametes having a different marker than their own. This gamete reco
Graph neural networks trained to predict observable dynamics can be used to decompose the temporal activity of complex heterogeneous systems into simple, interpretable representations. Here we apply this framework to simulated neural assemblies with thousands of neurons and demonstrate that it can j
The quality and consistency of training data remain critical bottlenecks for protein-ligand binding prediction. Public affinity datasets, aggregated from thousands of labs and assay formats, introduce biases that limit model generalization and complicate evaluation. DNA-encoded chemical libraries (D
The crawling motility of many eukaryotic cells is driven by filamentous actin (F-actin), and regulated by a network of signaling proteins and lipids (including small GTPases). The tangle of positive and negative feedback loops gives rise to various experimentally observed dynamic patterns (``actin w
Motivation: mtDNA distance matrices are standard inputs for distance-based phylogeny, but computing all pairwise alignments is costly. Missing entries can degrade inferred topology and branch lengths, and generic matrix-completion methods may disrupt tree-like (ultrametric) structure. Results: We
Richard A. Mathies is professor emeritus of Chemistry at the University of California, Berkeley. In this contribution he summarizes his journey through microfluidics over the past 30 years from the invention of Capillary Array Electrophoresis in the 1990s to recent attempts to launch a microfluidic
We consider a slight modification to the monocyte and T-lymphocyte boundary conditions of Little et al. (PLoS Comput Biol 2009 5(10) e1000539) and derive alternative parameter estimates. No changes to the results and conclusions of the paper of Little et al. (PLoS Comput Biol 2009 5(10) e1000539) ar
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss curvature'K'enters. The model suggests a novel point-like placeme
Computational analyses of, e.g., genomic, proteomic, or metabolomic data, commonly result in one or more sets of candidate genes, proteins, or enzymes. These sets are often the outcome of clustering algorithms. Subsequently, it has to be tested if, e.g., the candidate gene-products are members of kn
Homologous proteins have similar three-dimensional structures and biological functions that shape their sequences. The resulting coevolution-driven correlations underlie methods from Potts models to AlphaFold, which infer protein structure and function from sequences. Using a minimal model, we show
Single-cell RNA sequencing (scRNA-seq) data exhibit strong and reproducible statistical structure. This has motivated the development of large-scale foundation models, such as TranscriptFormer, that use transformer-based architectures to learn a generative model for gene expression by embedding gene
The paper titled ''Global gridded population datasets systematically underrepresent rural population'' by Josias Láng-Ritter et al. provides a valuable contribution to the discourse on the accuracy of global population datasets, particularly in rural areas. We recognize the efforts put into this res
The thermoregulation system in animals removes body heat in hot temperatures and retains body heat in cold temperatures. The better the animal removes heat, the worse the animal retains heat and visa versa. It is the balance between these two conflicting goals that determines the mammal's size, hear
Understanding the dynamic nature of brain connectivity is critical for elucidating neural processing, behavior, and brain disorders. Traditional approaches such as sliding-window correlation (SWC) characterize time-varying undirected associations but do not resolve directional interactions, limiting
Saliency maps are increasingly used as emph{design guidance} in siRNA efficacy prediction, yet attribution methods are rarely validated before motivating sequence edits. We introduce a textbf{pre-synthesis gate}: a protocol for emph{counterfactual sensitivity faithfulness} that tests whether mutatin
I propose that the need for sleep and the occurrence of dreams are intimately linked to the physical processes underlying the continuing replacement of cells and renewal of biomolecules during the lives of higher organisms. Since one major function of our brains is to enable us to react to attack, t
Synthesis of the biological 'energy currency molecule' adenosine triphosphate ATP is accomplished by FoF1-ATP synthase. In the plasma membrane of Escherichia coli, proton-driven rotation of a ring of 10 c subunits in the Fo motor powers catalysis in the F1 motor. While F1 uses 120 degree stepping, F
We analyze a model of interacting agents (e.g. prebiotic chemical species) which are represended by nodes of a network, whereas their interactions are mapped onto directed links between these nodes. On a fast time scale, each agent follows an eigendynamics based on catalytic support from other nodes
Metapopulation models describing cities with different populations coupled by the travel of individuals are of great importance in the understanding of disease spread on a large scale. An important example is the Rvachev-Longini model [{it Math. Biosci.} {bf 75}, 3-22 (1985)] which is widely used in
We work in the context of the infinitely many alleles model. The allelic partition associated with a coalescent process started from n individuals is obtained by placing mutations along the skeleton of the coalescent tree; for each individual, we trace back to the most recent mutation affecting it a
An endogenous molecular-cellular network for both normal and abnormal functions is assumed to exist. This endogenous network forms a nonlinear stochastic dynamical system, with many stable attractors in its functional landscape. Normal or abnormal robust states can be decided by this network in a ma
A k-noncrossing RNA pseudoknot structure is a graph over ${1,...,n}$ without 1-arcs, i.e. arcs of the form (i,i+1) and in which there exists no k-set of mutually intersecting arcs. In particular, RNA secondary structures are 2-noncrossing RNA structures. In this paper we prove a central and a local
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D physical distance between pairwise labeled genomic positions i
Cryo-electron tomography (cryo-ET) provides a unique window into molecular organization in cellular environments (in situ). However, the interpretation of molecular structural information is complicated by several intrinsic properties of cryo-ET data, such as noise, missing wedge, and continuous con
Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of species), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so to construct such a netw
We show that the critical mass M_c=8pi of bacterial populations in two dimensions in the chemotactic problem is the counterpart of the critical temperature T_c=GMm/4k_B of self-gravitating Brownian particles in two-dimensional gravity. We obtain these critical values by using the Virial theorem or b
Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (Austin model 1) methods. As distinct from previous calculations, fo
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a site-dependent process. Localized modes of nonlinear origin form spo
Since 1984, electric cell-substrate impedance sensing (ECIS) has been used to monitor cell behavior in tissue culture and has proven sensitive to cell morphological changes and cell motility. We have taken ECIS measurements on several cultures of non-cancerous (HOSE) and cancerous (SKOV) human ovari
To be practical for real-life applications, models for brain-computer interfaces must be easily and quickly deployable on new subjects, effective on affordable scanning hardware, and small enough to run locally on accessible computing resources. To directly address these current limitations, we intr
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