Analyzing ion distributions around DNA

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A search for heavy, long-lived, charged particles with large ionization energy loss within the silicon tracker of the CMS experiment is presented. A data set of proton-proton collisions at a center of mass energy at s = 13 TeV, collected in 2017 and 2018 a ...

As large, data-driven artificial intelligence models become ubiquitous, guaranteeing high data quality is imperative for constructing models. Crowdsourcing, community sensing, and data filtering have long been the standard approaches to guaranteeing or imp ...

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

We propose a novel approach to evaluating the ionic Seebeck coefficient in electrolytes from relatively short equilibrium molecular dynamics simulations, based on the Green-Kubo theory of linear response and Bayesian regression analysis. By exploiting the ...

Gels made of telechelic polymers connected by reversible cross-linkers are a versatile design platform for biocompatible viscoelastic materials. Their linear response to a step strain displays a fast, near-exponential relaxation when using low-valence cros ...

The probability of detecting technosignatures (i.e., evidence of technological activity beyond Earth) increases with their longevity, or the time interval over which they manifest. Therefore, the assumed distribution of longevities has some bearing on the ...

The experimental fusion reactor ITER will feature two (or three) heating neutral beam injectors (NBI) capable of delivering 33(or 50) MW of power into the plasma. A NBI consists of a plasma source for production of negative ions (extracted negative ion cur ...

Under resource constraints, LLMs are usually fine- tuned with additional knowledge using Parameter Efficient Fine-Tuning (PEFT), using Low-Rank Adaptation (LoRA) modules. In fact, LoRA injects a new set of small trainable matrices to adapt an LLM to a new ...

Under resource constraints, LLMs are usually fine-tuned with additional knowledge using Parameter Efficient Fine-Tuning (PEFT), using Low-Rank Adaptation (LoRA) modules. In fact, LoRA injects a new set of small trainable matrices to adapt an LLM to a new t ...

Atomistic simulations performed with a family of model potential with tunable hardness have proven to be a great tool for advancing the understanding of wear processes at the asperity level. They have been instrumental in finding a critical length scale, w ...

In this thesis, we conduct a comprehensive investigation into structural instabilities of both elastic and magneto-elastic beams and shells, resulting in a creative proposal to design a programmable braille reader. Methodologically, we combine numerical si ...

Despite the widespread empirical success of ResNet, the generalization properties of deep ResNet are rarely explored beyond the lazy training regime. In this work, we investigate scaled ResNet in the limit of infinitely deep and wide neural networks, of wh ...

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

Two related methods for inverting line-integrated measurements are presented in this research paper in the context of the recent deuterium-tritium experiments in the JET tokamak. Unlike traditional methods of tomography, these methods rely on making use of ...

One major challenge in distributed learning is to efficiently learn for each client when the data across clients is heterogeneous or non iid (not independent or identically distributed). This provides a significant challenge as the data of the other client ...

Linear-Quadratic-Gaussian (LQG) control is a fundamental control paradigm that is studied in various fields such as engineering, computer science, economics, and neuroscience. It involves controlling a system with linear dynamics and imperfect observations ...

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

BackgroundAging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain ...

Analyzing ion distributions around DNA

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Search for heavy long-lived charged particles with large ionization energy loss in proton-proton collisions at s = 13 TeV

Extensions of Peer Prediction Incentive Mechanisms

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Seebeck Coefficient of Ionic Conductors from Bayesian Regression Analysis

Valence can control the nonexponential viscoelastic relaxation of multivalent reversible gels

Technosignatures Longevity and Lindy's Law

Optimizing the ITER NBI ion source by dedicated RF driver test stand

Beyond fine-tuning: LoRA modules boost near-OOD detection and LLM security

Beyond fine-tuning: LoRA modules boost near-OOD detection and LLM security

A story of two transitions: From adhesive to abrasive wear and from ductile to brittle regime

Instabilities in Elastic and Magneto-Elastic Beams and Shells: from Shell Buckling to the Design of a Programmable Braille Reader

Generalization of Scaled Deep ResNets in the Mean-Field Regime

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Regressive Tomography and Direct Regressive Reconstruction: A Research Note

Personalized Privacy-Preserving Distributed Learning on Heterogeneous Data

Distributionally Robust Linear Quadratic Control

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Secondary structure of the human mitochondrial genome affects formation of deletions