High-sensitive protein analysis by FESI-CEMALDI-MS

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We develop new tools to study landscapes in nonconvex optimization. Given one optimization problem, we pair it with another by smoothly parametrizing the domain. This is either for practical purposes (e.g., to use smooth optimization algorithms with good g ...

Orthogonal group synchronization is the problem of estimating n elements Z(1),& mldr;,Z(n) from the rxr orthogonal group given some relative measurements R-ij approximate to Z(i)Z(j)(-1). The least-squares formulation is nonconvex. To avoid its local minim ...

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

In this paper, we present a new parameterization and optimization procedure for minimizing the weight of ribbed plates. The primary goal is to reduce embodied CO2 in concrete floors as part of the effort to diminish the carbon footprint of the construction ...

We present a combination technique based on mixed differences of both spatial approximations and quadrature formulae for the stochastic variables to solve efficiently a class of optimal control problems (OCPs) constrained by random partial differential equ ...

Distributed learning is the key for enabling training of modern large-scale machine learning models, through parallelising the learning process. Collaborative learning is essential for learning from privacy-sensitive data that is distributed across various ...

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 ...

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 ...

A method for optimizing at least one of a geometry, an implantation procedure, and/or stimulation protocol of one or more electrodes for an electrical stimulation of a target structure in a nervous system of a living being by a computer device, the method ...

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...

We propose ordering-based approaches for learning the maximal ancestral graph (MAG) of a structural equation model (SEM) up to its Markov equivalence class (MEC) in the presence of unobserved variables. Existing ordering-based methods in the literature rec ...

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

Omnidirectional video streaming is usually implemented based on the representations of tiles, where the tiles are obtained by splitting the video frame into several rectangular areas and each tile is converted into multiple representations with different r ...

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

Designing turbocompressors is a complex and challenging task, as it involves balancing conflicting objectives such as efficiency, stability, and robustness against manufacturing deviations. This paper proposes an integrated design methodology for turbocomp ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

In this paper, we present a spatial branch and bound algorithm to tackle the continuous pricing problem, where demand is captured by an advanced discrete choice model (DCM). Advanced DCMs, like mixed logit or latent class models, are capable of modeling de ...

High-sensitive protein analysis by FESI-CEMALDI-MS

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The effect of smooth parametrizations on nonconvex optimization landscapes

BENIGN LANDSCAPES OF LOW-DIMENSIONAL RELAXATIONS FOR ORTHOGONAL SYNCHRONIZATION ON GENERAL GRAPHS

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Mesh-based topology, shape and sizing optimization of ribbed plates

A Combination Technique for Optimal Control Problems Constrained by Random PDEs

Optimization Algorithms for Decentralized, Distributed and Collaborative Machine Learning

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

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

A method and system for optimizing design, implantation, and stimulation protocols of electrodes stimulating the nervous system

Development of tools and methods for protein identification: From single molecules to in vivo applications

Opportunities and challenges in design and optimization of protein function

Predicting protein interactions using geometric deep learning on protein surfaces

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

Novel Ordering-based Approaches for Causal Structure Learning in the Presence of Unobserved Variables

De novo protein design by inversion of the AlphaFold structure prediction network

Quality-Constrained Encoding Optimization for Omnidirectional Video Streaming

De novo design of protein interactions with learned surface fingerprints

An Integrated Approach to Designing Robust Turbocompressors on Gas Bearings Through Surrogate Modeling and Constrained Multi-Objective Optimization

De novo designed proteins: a study in engineering novel folds and functions

A Spatial Branch and Bound Algorithm for Continuous Pricing with Advanced Discrete Choice Demand Modeling