Related papers: Efficient fidelity control by stepwise nucleotide …
Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Conformal selection (CS) uses calibration data to identify test inputs whose unobserved outcomes are likely to satisfy a pre-specified minimal quality requirement, while controlling the false discovery rate (FDR). Existing methods fix the…
One of the most important lessons from the success of deep learning is that learned representations tend to perform much better at any task compared to representations we design by hand. Yet evolution of evolvability algorithms, which aim…
Feature selection is a critical task in machine learning and statistics. However, existing feature selection methods either (i) rely on parametric methods such as linear or generalized linear models, (ii) lack theoretical false discovery…
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these…
Direct fidelity estimation (DFE) is a famous tool for estimating the fidelity with a target pure state. However, such a method generally requires exponentially many sampling copies due to the large magic of the target state. This work…
Bicontinuous microstructures are essential to the function of diverse natural and synthetic systems. Their synthesis has been based on two approaches: arrested phase separation or self-assembly of block copolymers. The former is attractive…
Machine- and deep-learning approaches for biological sequences depend critically on transforming raw DNA, RNA, and protein FASTA files into informative numerical representations. However, this process is often fragmented across multiple…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
When proving the correctness of a method for slicing probabilistic programs, it was previously discovered by the authors that for a fixed point iteration to work one needs a non-standard starting point for the iteration. This paper presents…
Efficient exploitation of exascale architectures requires rethinking of the numerical algorithms used in many large-scale applications. These architectures favor algorithms that expose ultra fine-grain parallelism and maximize the ratio of…
Monitoring the kinetics and conformational dynamics of single enzymes is crucial in order to better understand their biological functions as these motions and structural dynamics are usually unsynchronized among the molecules. Detecting the…
When selecting from a list of potential candidates, it is important to ensure not only that the selected items are of high quality, but also that they are sufficiently dissimilar so as to both avoid redundancy and to capture a broader range…
Several methods for preparing well equilibrated melts of long chains polymers are studied. We show that the standard method in which one starts with an ensemble of chains with the correct end-to-end distance arranged randomly in the…
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear…
Template based single step retrosynthesis predicts reactants by selecting and applying an explicit reaction template, making each prediction traceable to a chemical transformation rule. This is useful for synthesis planning, but template…
The goal of eQTL studies is to identify the genetic variants that influence the expression levels of the genes in an organism. High throughput technology has made such studies possible: in a given tissue sample, it enables us to quantify…