4,320 Works

Microscopically-derived modelling of quantum networks subject to multiple environments

Erik Gauger
The interplay between coherent and dissipative processes that governs both bio-inspired as well as engineered quantum networks supports a rich tapestry of non-equilibrium phenomena. These hold promise for enabling quantum-enhanced light harvesting, molecular electronics, generation of thermopower, and nanoscale sensing. A theoretical challenge consists of developing well-founded and tractable models for exploring the dynamics of systems that are simultaneously strongly coupled to more than one environment, for instance through interactions with surrounding electromagnetic and vibrational...

Classical emulation of quantum-coherent thermal machines

Luis A. Correa
The performance enhancements observed in various models of continuous quantum thermal machines have been linked to the buildup of coherences in a preferred basis. But, is this connection always an evidence of 'quantum-thermodynamic supremacy' By force of example, we show that this is not the case. In particular, we compare a power-driven three-level continuous quantum refrigerator with a four-level combined cycle, partly driven by power and partly by heat. We focus on the weak driving...

Evolution in space

Daniel Weissman
Most populations are spread over spatial ranges much bigger than any one individual will explore in its lifetime. How does the simple fact of this spatial structure affect adaptive evolution and genetic diversity We quantify how space interacts with recombination (sex) to slow down or speed up adaptation by changing the amount of clonal interference among beneficial mutations, and to change how adaptation reshapes neutral diversity through genetic hitchhiking. We also show how the spatial...

Nonlinear Quantum Adiabatic Approximation

Alain Joye
We consider the adiabatic limit of a nonlinear Schrödinger equation in which the Hamiltonian depends on time and on a finite number of components of the wave function. We show the existence of instantaneous nonlinear eigenvectors and of solutions which remain close those, up to a rapidly oscillating phase in the adiabatic regime. Consequences on the energy content of the solutions are spelled out. $$ $$ This is joint work with Clotilde Fermanian

Quantum resonance theory of open system dynamics

Marco Merkli
We present a mathematical method allowing to prove the validity of the Markovian approximation for an $N$-level quantum system in contact with thermal reservoirs. The true system dynamics is approximated by a completely positive, trace preserving dynamical group $f\!or\ all\ times\ t\ge0$, provided the system-reservoir coupling $\lambda$ is small but fixed. No weak coupling condition $\lambda^2 t\lesssim {\rm const.}$ is imposed.

Introduction to Jupyter and Syzygy

Michael Lamoureux
An overview of the Jupyter project, including the PIMS Syzygy program, and how Jupyter can be used in the classroom.

Breaking the Rule of Objectivity : A Journalist in Haiti

Catherine Porter
Porter’s international reporting includes countries such as Senegal, Guatemala, Cuba and, most notably, Haiti. Prior join The New York Times in 2017, she was a columnist and feature writer for the Toronto Star. Porter was among the journalists who arrived in Port-au-Prince shortly after the 2010 earthquake, and has returned to the country to report on its reconstruction efforts. Her latest book about that experience, A Girl Named Lovely, reflects her work as a “narrative...

Gertrude Bell in Focus : Exploring and Photographing the Middle East

Lisa Cooper
Dr. Lisa Cooper’s research interests include the history of archaeological exploration and archaeological practice in “Greater Mesopotamia” (ancient Iraq, Syria, Iran and Turkey), particularly in the early 20th century. She is currently part of the Central Zagros Archaeology Project in Iraqi Kurdistan. Dr. Cooper has also done extensive research into the life and work of the early 20th century English explorer and archaeologist Gertrude Bell, about whom she wrote in her book In Search of...

The Society of Crows

Robert Butler
Dr. Robert Butler’s research interests include the social behaviour of crows, ecology of herons, and migration of birds. He has delivered public lectures at scientific conferences in Canada and around the world. Dr. Butler co-produced two films: The Perfect State, and Returning about the relationship between nature and culture. He is a fellow of The Explorers Club, the Royal Canadian Geographic Society, the American Ornithologists Union, and Signature Member of Artists for Conservation. Dr. Butler...

Right-Wing vs Left-Wing Populism : Lessons from Venezuela and the United States

Javier Corrales
Dr. Corrales’ research focuses on democratization, presidential powers, foreign policy, and sexuality. He has published extensively on Venezuela, Cuba, and Argentina for academic outlets as well as The New York Times. Among his several books, Dr. Corrales is co-author of Dragon in the Tropics: Venezuela and the Legacy of Hugo Chávez, and Fixing Democracy: Why Constitutional Change Often Fails to Enhance Democracy in Latin America. He is also the co-editor of The Politics of Sexuality...

The Art of the Impossible : A Life in Canadian Publishing

Scott McIntyre
For over 40 years Dr. Scott McIntyre has been an active promoter of the Canadian cultural industry. He was a founding partner of Douglas & McIntyre Publishers, which during his tenure published some 2000 books. His contributions to Canadian culture have brought him many honours, including an honorary degree from Simon Fraser University, the inaugural IVY Award for his substantial contributions to Canadian publishing from the International Festival of Authors in Toronto, and the 2016...

Quirky Past, Uncertain Future : A Prescription for Treating Canada’s Aging Medicare System

Andre Picard
André Picard has written extensively on Canadian public health issues. His most recent books include A Matter of Life and Death: Public Health Issues in Canada, and The Path to Health Care Reform: Policies and Politics. He has been the recipient of the Canadian Nurses’ Association Award of Excellence for Health Care Reporting, the Nursing in the Media Award of the Registered Nurses Association of Ontario, the International Media Prize of Sigma Theta Tau (Nursing...

Convex Integration and Compressible Euler System

Eduard Feireisl

Uniqueness of Solutions Versus Convex Integration for Conservation Laws in One Space Dimension

Sam Krupa

Computational model of kinetochore-microtubule attachments

Tamara Bidone
The ability of cells to separate chromosomes during mitosis is critical to several phases of their physiology. Chromosome segregation is mediated by spindle microtubules that attach to mitotic kinetochores via a dynamic protein interface, which includes Ndc80 and its accessory proteins, Ska, Cdt1 and ch-TOG [1-3]. The Ndc80 complex forms the core component of the attachment sites while Ska, Cdt1 and ch-TOG binds kinetochores via the Ndc80 complex. From prometaphase to metaphase, the kinetochore levels...

Graph Theory in Orthology Detection

Maribel Hernández Rosales
During evolution genes go throw many events, such as duplication, speciation, loss, horizontal gene transfer, among others. Two genes are said to be paralogs if they are the product of a duplication event, and orthologs if they are the product of a speciation event. The distinction of paralogs and orthologs is an important problem in comparative and evolutionary genomics. Moreover, orthology detection is a first step towards any functional annotation study. The evolutionary history of...

A Global Subspace Optimization Algorithm for Minimum Energy Molecular Cluster Conformation

Zhiyun Wu
We consider the problem to obtain the optimal conformation of a given molecular cluster with the lowest possible potential energy. This problem has been studied as a test case for global optimization algorithms, and considered as a starting point for the study of more complicated conformational problems such as protein folding through potential energy minimization. Here we propose a global subspace optimization algorithm for the solution of the problem, with the variables of the energy...

Limits of performance for protein side chain packers

Carlos Brizuela
To date, it is possible to design proteins with an improved function starting from known scaffolds. This design applies to the enhancement of enzymatic capabilities, inhibitors of protein-protein interactions, among others [1]. The next generation for the design of functional proteins will be guided by the approach known as template-free design. The goal of this approach is to design a sequence of amino acids that will have a predefined function. A more conservative approach seeks...

Experimental study of the pre-gelation behaviour of composite prepreg : [supplementary material]

Caitlin Duffner
The attached file is a supplements to the author’s master’s thesis at https://circle.library.ubc.ca/handle/2429/72979

The water we call home : five generations of Indigenous women's resistance along the Salish Sea : [supplementary material]

Jessica Wynne Hallenbeck
The attached file is a supplement to the author’s doctoral dissertation at https://circle.library.ubc.ca/handle/2429/72961

Pruning false positives cases from small molecule docking results using machine learning techniques

Marcelino Arciniega
Over the last three decades, Computer Aided Drug Design (CADD) has positioned as one of the more useful approaches aiding the research at early stages of drug discovery process [1]. Particularly, small molecule docking algorithms have been employed exhaustively to identify the possible atomic interactions, between the protein target and a suggested small molecule, that support the formation of the protein-ligand complex. This evaluation is performed by employing a scoring function that relates geometric patterns...

Effect of Phosphorylation and Mutation to Asp and Glu on the Conformational Landscape of an Intrinsically Disordered Region

Nina Pastor
Intrinsically disordered proteins are notorious for their conformational flexibility and capacity for interaction with different targets by acquiring distinct conformations depending on the specifics of the binding site. They can also engage in specific interactions without loosing conformational freedom, forming fuzzy complexes. The particular conformations favored by these proteins can be tuned by posttranslational modifications, such as phosphorylation. A common experimental strategy to study the effect of phosphorylation is to perform mutations of the modified...

SimRNA: a coarse-grained method for RNA 3D structure modeling - new ideas accounting for on non-canonical base pairing

Michał Boniecki
The molecules of the ribonucleic acid (RNA) perform a variety of vital roles in all living cells. Their biological function depends on their structure and dynamics, both of which are difficult to experimentally determine but can be theoretically inferred based on the RNA sequence. SimRNA [1] is one of the computational methods for molecular simulations of RNA 3D structure formation. The method is based on a simplified (coarse-grained) representation of nucleotide chains, a statistically derived...

Structure prediction of mono- and oligomeric tarets using the physics-based coarse-grained UNRES force field and information from databases â CASP13/CAPRI46

Agnieszka Karczynska
The results of blind prediction of the structures of monomeric and oligomeric proteins obtained in the recent CASP/CAPRI experiment by the KIAS-Gdansk/Czaplewski groups, by using the physics-based coarse-grained UNRES force field [1] and information from databases are presented. For both monomeric and oligomeric targets, the methodology of the KIAS-Gdansk/Czaplewski groups included extensive conformational search by means of the Multiplexed Replica Exchange Molecular Dynamics (MREMD) simulations [2] with the UNRES force field [3], with geometry restraints...

Chemical shifts based structural ensemble generation for intrinsically disordered proteins: A case study

Yi He
About a third of the proteome consists of intrinsically disordered proteins (IDPs) that fold, whether fully or partially, upon binding to their partners [1]. IDPs use their inherent flexibility to play key regulatory roles in many biological processes [2]. Such flexibility makes their structural analysis extremely challenging, being nuclear magnetic resonance (NMR) the most suitable high-resolution technique. However, conventional NMR structure determination methods, which seek to determine a single high-resolution structure [3], are inadequate for...

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