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Microstructural Kinetics Group

Department of Materials Science & Metallurgy
 

Wed 03 Nov 14:30: Coarse-Graining Markov State Models

School of Physical Sciences - Mon, 18/10/2021 - 15:39
Coarse-Graining Markov State Models

Markov state models (MSMs) provide a useful framework for understanding the kinetics of highly complex systems. Accordingly, MSM -based methods are increasingly popular to analyse and drive molecular dynamics simulations, including biasing and unbiasing simulations to enhance sampling. However, the dimensionality of these models is still very large when we consider a space of selected discretised collective variables. We developed kinetics-based coarse graining methods to identify metastable and transition states using variational objective functions: the second eigenvalue corresponding to the slowest relaxation time, and the Kemeny constant, corresponding to the sum of all relaxation times of the system. We show that these objective functions are closely related to mean first passage times that may be easier available in various applications of complex networks beyond molecular simulations.

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Thu 10 Mar 16:00: Title to be confirmed

School of Physical Sciences - Mon, 18/10/2021 - 12:02
Title to be confirmed

Abstract not available

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Tue 19 Oct 17:00: Title to be confirmed

School of Physical Sciences - Mon, 18/10/2021 - 10:36
Title to be confirmed

Please refer to the speaker’s website for more information.

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Wed 02 Feb 14:00: Machine learning with biomedical ontologies: applications in precision health Our intention is to deliver all Seminars in person, we will follow University Covid Guidance on this. Seminars are aimed mainly at MPhil CompBio students,...

School of Physical Sciences - Mon, 18/10/2021 - 10:15
Machine learning with biomedical ontologies: applications in precision health

The life sciences have invested significant resources in the development and application of semantic technologies to make research data accessible and interlinked, and to enable the integration and analysis of data. Utilizing the semantics associated with research data in data analysis approaches is often challenging. Now, novel methods are becoming available that combine symbolic methods and statistical methods in Artificial Intelligence. In my talk, I will show how to incorporate biological background knowledge in machine learning models for identification of gene-disease associations, genomic variants that are causative for heritable disorders, and to predict protein functions. The methods I describe are generic and can be applied in other domains in which biomedical ontologies and structured knowledge bases exist.

Our intention is to deliver all Seminars in person, we will follow University Covid Guidance on this. Seminars are aimed mainly at MPhil CompBio students, but are open to anyone who wishes to attend by pre-booking with the Administrator

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Wed 23 Feb 14:00: Mining for meaning in electronic health records; deep semantic normalisation for precision medicine and discovery. Our intention is to deliver all Seminars in person, we will follow University Covid Guidance on this. Seminars are...

School of Physical Sciences - Mon, 18/10/2021 - 09:55
Mining for meaning in electronic health records; deep semantic normalisation for precision medicine and discovery.

Electronic health records (EHRs) contain information critical to the realisation of the promise of personalised medicine, but also data essential for the discovery of the molecular basis of disease. Clinical information systems and EHRs were not developed for the discovery, integration and export of information, most being based on the concept of paper records going back to the 1990s. Consequently we find in EHRs information contained in administrative, diagnostic and procedure codes, which are highly structured and standardised, the results of investigative tests, ranging from blood chemistry to images, which might be regarded as partially structured information, and finally narrative reports of clinical encounters and discharge letters which are rich sources of information but completely unstructured. Reliably extracting and integrating these types of information is a huge challenge, but the ability to retrieve coded and quantitative data into a common symbolic framework opens up the possibility of connecting these data together with the large amounts of background knowledge now available.

I will discuss three approaches to extracting and using EHR information: the first uses the Komenti platform which is designed to extract information from free text into semantically formalised ontological annotations, the second is an approach to combine quantitative data into that same semantic framework. The third, a new resource, axiomatises ICD -10 terms uses the Human phenotype ontology for integration with existing knowledge and, for example, patient classification. The promise of these orthogonal approaches will be discussed.

Our intention is to deliver all Seminars in person, we will follow University Covid Guidance on this. Seminars are aimed mainly at MPhil CompBio students, but are open to anyone who wishes to attend by pre-booking with the Administrator

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Fri 15 Oct 13:00: Stabilizing relativistic fluids on slowly expanding cosmological spacetimes

School of Physical Sciences - Fri, 15/10/2021 - 14:50
Stabilizing relativistic fluids on slowly expanding cosmological spacetimes

On a background Minkowski spacetime, the relativistic Euler equations are known, for a relatively general equation of state, to admit unstable homogeneous solutions with finite-time shock formation. By contrast, such shock formation can be suppressed on background cosmological spacetimes whose spatial slices expand at an accelerated rate. The critical case of linear, ie zero-accelerated, spatial expansion, is not as well understood. In this talk, I will present two recent works concerning the relativistic Euler and the Einstein-Dust equations for geometries expanding at a linear rate. This is based on joint works with David Fajman, Todd Oliynyk and Max Ofner.

This will be a hybrid seminar; Zoom link information for remote participation is below

Topic: Friday GR Seminar Time: Oct 15, 2021 01:00 PM London

Join Zoom Meeting https://maths-cam-ac-uk.zoom.us/j/97331010435?pwd=c0FWU2hGUVRBd0lrbDNtcFd1c25EQT09

Meeting ID: 973 3101 0435 Passcode: 073244

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Wed 20 Oct 14:15: K-moduli for log Fano complete intersections

School of Physical Sciences - Thu, 14/10/2021 - 18:48
K-moduli for log Fano complete intersections

An important category of geometric objects in algebraic geometry is smooth Fano varieties, which have positive curvature. These have been classified in 1, 8 and 105 families in dimensions 1, 2 and 3 respectively, while in higher dimensions the number of Fano families is yet unknown, although we know that their number is bounded. An important problem is compactifying these families into moduli spaces via K-stability. In this talk, I will describe the compactification of the family of Fano threefolds, which is obtained by blowing up the projective space along a complete intersection of two quadrics, into a K-moduli space using Geometric Invariant Theory (GIT). A more interesting setting occurs in the case of pairs of varieties and a hyperplane section where the K-moduli compactifications tessellate depending on a parameter. In this case it has been shown recently that the K-moduli decompose into a wall-chamber decomposition depending on a parameter, but wall-crossing phenomena are still difficult to describe explicitly. Using GIT , I will describe an explicit example of wall-crossing in the K-moduli spaces, where both variety and divisor differ in the deformation families before and after the wall, given by log pairs of Fano surfaces of degree 4 and a hyperplane section.

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Wed 03 Nov 15:30: High-frequency fluctuations in Antarctic Bottom Water transport driven by Southern Ocean winds

School of Physical Sciences - Thu, 14/10/2021 - 16:38
High-frequency fluctuations in Antarctic Bottom Water transport driven by Southern Ocean winds

Northward flow of Antarctic Bottom Water (AABW) across the Southern Ocean comprises a key component of the global overturning circulation. Yet AABW transport remains poorly constrained by observations and state estimates, and there is presently no means of directly monitoring any component of the Southern Ocean overturning. However, AABW flow is dynamically linked to Southern Ocean surface circulation via the zonal momentum balance, offering potential routes to indirect monitoring of the transport. Exploiting this dynamical link, this study uses a dynamically self-consistent ocean state estimate (ECCOV4r4) to show that wind stress fluctuations drive large AABW transport fluctuations on time scales shorter than ~2 years, which comprise almost all of the transport variance. This connection occurs due to differing time scales on which topographic and interfacial form stresses respond to wind variability, likely associated with differences in barotropic vs. baroclinic Rossby wave propagation. These findings imply that AABW transport variability can largely be reconstructed from the surface wind stress alone.

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Wed 03 Nov 17:00: From the possibility to the certainty of a supermassive black hole

School of Physical Sciences - Thu, 14/10/2021 - 15:55
From the possibility to the certainty of a supermassive black hole

ANDREW CHAMBLIN MEMORIAL LECTURE 2021

Join Professor Andrea Ghez (University of California, Los Angeles), 2020 Nobel Laureate in Physics, to learn about new developments in the study of supermassive black holes.

Through the capture and analysis of twenty years of high-resolution imaging, the UCLA Galactic Center Group has moved the case for a supermassive black hole at the centre of our galaxy from a possibility to a certainty, and provided the best evidence to date for the existence of these truly exotic objects.

Recent observations have revealed an environment around the black hole that is quite unexpected – young stars where there should be none; a lack of old stars where there should be many; and a puzzling new class of objects. Professor Ghez will explore how this work is providing insight into how black holes grow and the role that they play in regulating the growth of their host galaxies.

Register for the event here: https://www.maths.cam.ac.uk/events/chamblin2021

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Fri 15 Oct 13:00: Stabilizing relativistic fluids on slowly expanding cosmological spacetimes

School of Physical Sciences - Thu, 14/10/2021 - 14:49
Stabilizing relativistic fluids on slowly expanding cosmological spacetimes

On a background Minkowski spacetime, the relativistic Euler equations are known, for a relatively general equation of state, to admit unstable homogeneous solutions with finite-time shock formation. By contrast, such shock formation can be suppressed on background cosmological spacetimes whose spatial slices expand at an accelerated rate. The critical case of linear, ie zero-accelerated, spatial expansion, is not as well understood. In this talk, I will present two recent works concerning the relativistic Euler and the Einstein-Dust equations for geometries expanding at a linear rate. This is based on joint works with David Fajman, Todd Oliynyk and Max Ofner.

This will be a hybrid seminar; Zoom link information for remote participation is below

Topic: Friday GR Seminar Time: Oct 15, 2021 01:00 PM London

Join Zoom Meeting https://maths-cam-ac-uk.zoom.us/j/97331010435?pwd=c0FWU2hGUVRBd0lrbDNtcFd1c25EQT09

Meeting ID: 973 3101 0435 Passcode: 073244

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Fri 05 Nov 13:00: Quasi-local mass of the Kerr black hole horizon

School of Physical Sciences - Thu, 14/10/2021 - 14:48
Quasi-local mass of the Kerr black hole horizon

Abstract not available

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Fri 12 Nov 16:00: TBC

School of Physical Sciences - Thu, 14/10/2021 - 10:03
TBC

Abstract not available

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Wed 20 Oct 14:30: Nucleation in first order phase transitions starting from the top

School of Physical Sciences - Wed, 13/10/2021 - 16:10
Nucleation in first order phase transitions starting from the top

The first step of the transition from a mestastable arrangement of particles to a stable one is the nucleation of the latter somewhere within the former. We use computer simulations to investigate this phenomenon. The common denominator in all our studies is that we start with the nucleus already formed, an approach we call “Seeding”. Although information on the path leading to the formation of the nucleus is obviously lost, we gain a wide overview on the nucleation rate trend, which provides physical understanding of the nucleation behaviour upon changes of the thermodynamic conditions. With this approach, for instance, we have been able to understand the effect of pressure [1,2] or solutes [3,4] on ice nucleation from supercooled water; investigate the irreconcilable discrepancies between experiments and simulations of hard sphere crystallization [5]; or even propose a new way of polymorph selection in charged colloids [6]. I will discuss these interesting phase transition phenomena in my presentation introducing first the basic theoretical concepts to understand nucleation.

[1] Espinosa, Jorge R.; Zaragoza, Alberto; Rosales-Pelaez, Pablo; Navarro, Caridad; Valeriani, Chantal; Vega, Carlos; Sanz, Eduardo; Physical Review Letters, 117, 135702, 2016

[2] V Bianco, PM de Hijes, CP Lamas, E Sanz, C Vega, Physical Review Letters 126 (1), 015704, 2021

[3] Soria, G. D., Espinosa, J. R., Ramirez, J., Valeriani, C., Vega, C., & Sanz, E.; The Journal of Chemical Physics, 148(22), 222811., 2018

[4] JR Espinosa, GD Soria, J Ramirez, C Valeriani, C Vega, E Sanz; The Journal of Physical Chemistry Letters 8 (18), 4486-4491, 2017

[5] JR Espinosa, C Vega, C Valeriani, D Frenkel, E Sanz, Soft matter 15 (47), 9625-9631, 2019

[6] I Sanchez-Burgos, A Garaizar, C Vega, E Sanz, JR Espinosa, Soft Matter 17 (3), 489-505, 2021

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Wed 20 Oct 16:30: Statistics Clinic Michaelmas 2021 I

School of Physical Sciences - Wed, 13/10/2021 - 10:32
Statistics Clinic Michaelmas 2021 I

If you would like to participate, please fill in the following form. The deadline for signing up of a remote session is 3pm on Monday the 18th of October. Subject to availability of members of the Statistics Clinic team, we will confirm your in-person or remote appointment.

This event is open only to members of the University of Cambridge (and affiliated institutes). Please be aware that we are unable to offer consultations outside clinic hours.

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Fri 12 Nov 13:00: Title to be confirmed

School of Physical Sciences - Wed, 13/10/2021 - 09:17
Title to be confirmed

Abstract not available

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Fri 15 Oct 16:00: The Geometric SMEFT description of curved Higgs Field Space(s) - Michael Trott

School of Physical Sciences - Wed, 13/10/2021 - 08:29
The Geometric SMEFT description of curved Higgs Field Space(s) - Michael Trott

The seminar will take place in the Potter Room at DAMPT and will be broadcast via Zoom here.

Abstract: In recent years, the effective field theory approach to the Standard Model, the SMEFT , has been used to study LHC data with ever increasing theoretical precision and sophistication. However, the complexity of this theory lead to several barriers to substantial theoretical progress. In particular, the explosion in the number of parameters in the SMEFT as a function of operator mass dimension, and the technical challenge or reformulating SM predictions consistently into the SMEFT were very serious problems, that called into question the possible success and value of the SMEFT physics program over the long term. I will discuss how these challenges have been overcome. The key point leading to this advance is the understanding that the projection of curved scalar field spaces generated by the Higgs onto a naive flat field space understanding implicitly embedded into the usual SMEFT Lagrangian and approach was the root cause of many problems, technical challenges and confusions. Many outstanding issues have now been addressed and immediately overcome by reformulating the SMEFT noting its curved scalar field space(s) – in the Geometric SMEFT . Some examples of the benefits of this approach will be presented, and explained.

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Tue 02 Nov 14:00: Empirical measures, geodesic lengths, and a variational formula in first-passage percolation

School of Physical Sciences - Tue, 12/10/2021 - 23:16
Empirical measures, geodesic lengths, and a variational formula in first-passage percolation

We consider the standard first-passage percolation model on Z^d, in which each edge is assigned an i.i.d. nonnegative weight, and the passage time between any two points is the smallest total weight of a nearest-neighbor path between them. This induces a random ``disordered” geometry on the lattice. Our primary interest is in the empirical measures of edge-weights observed along geodesics in this geometry, say from 0 to [n\xi], where \xi is a fixed unit vector. For various dense families of edge-weight distributions, we prove that these measures converge weakly to a deterministic limit as n tends to infinity. The key tool is a new variational formula for the time constant. In this talk, I will derive this formula and discuss its implications for the convergence of both empirical measures and lengths of geodesics.

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