Presentation – Soft Matter Lab

CHAIR seminar by C. Martinez on 27 March 2024

Introduction to G-Research, a quantitative research and technology company
Charles Martinez
G-Research, London, UK
27 March 2024
12:30-14:30
PJ
Organized by the CHAIR theme AI for Scientific Data Analysis

Bio: Dr Charles Martinez is the Academic Relations Manager at G-Research. Charles started his studies as a physicist at University Portsmouth Physics department’s MPhys programme, and later completed a PhD in Phonon interactions in Gallium Nitride nanostructures at the University of Nottingham. Charles then worked on indexing and abstract databases at the Institution for Engineering and Technology (IET) before moving into sales in 2010. Charles’ previous role was as Elsevier’s Key Account Manager, managing sales and renewals for the UK Russell Group institutions, Government and Funding body accounts, including being one of the negotiators in the recent UK ScienceDirect Read and Publish agreement. Since leaving Elsevier Charles is dedicated to forming beneficial partnerships between G-Research and Europe’s top institutions, and is living in Cambridge, UK.

Seminar by C. Martinez on 27 March 2024

Learning about G-Research: thinking about strategies in quantitative finance
Charles Martinez
G-Research, London, UK
27 March 2024
10:00-11:30
FB (Fysik-Huset)

We are a leading quantitative research and technology company based in London. Day to day we use a variety of quantitative techniques to predict financial markets from large data sets worldwide. Mathematics, statistics, machine learning, natural language processing and deep learning is what our business is built on. Our culture is academic and highly intellectual. In this seminar I will explain our background, current AI research applications to finance and our ongoing outreach, recruitment and grants programme. The seminar will be aimed at students who are curious about quant finance or interested in internship opportunities. We will also play an interactive game. The game will last around 1 hour and there will be prizes for the Top 3 scores (amazon vouchers – £100). Dice will be provided.

Seminar by W. Ahmed on 13 March 2024

A schematic of a passive particle immersed in an active bath experiencing non-equilibrium fluctuations. *(Illustration by W. Ahmed)*

Emergent behavior in active biological matter
Wylie Ahmed
Laboratoire de Physique Theorique, Toulouse (France) and California State University, Fullerton (USA)

13 March 2024, 12:30, Nexus

Motivated by nucleus centering in mouse oocytes, we explore a different type of biological active matter. We investigate the stochastic force fluctuations of micro swimmers in two scenarios: (1) a single swimmer navigating through a passive fluid; (2) a dense suspension of swimmers surrounding a passive tracer. By direct force measurement using optical tweezers we show that the force trajectory of an individual micro swimmer exhibits rich oscillatory dynamics that vary in time. Interestingly, when these highly fluctuating force dynamics are analyzed using the framework of stochastic thermodynamics we recover energy dissipation rates in agreement with time-averaged fluid dynamics studies. For a dense suspension of swimmers serving as an active bath for a passive tracer we observe both shear thinning and thickening, which depends on Peclet number, and enhanced diffusion of our tracer by a factor of 2. We estimate the energy transfer rate from the active bath to the passive tracer. These two scenarios allow us to explore energy exchange between an active swimmer in a passive bath and a passive tracer in an active bath.

Berenice García Rodríguez presented her half-time seminar on 8 March 2024

Berenice García Rodríguez (right) and opponent Dr. Hana Jungová (left). *(Photo by J. P. Ramírez)*

Berenice García Rodríguez completed the first half of her doctoral studies, and she defended her half-time on the 8th of March 2024.

The presentation, “Quantitative Analysis of Nanoparticle Properties Using Optical Scattering Techniques,” was held in a hybrid format, with part of the audience in the Nexus room and the rest connected through Zoom. The half-time consisted of a presentation about her past and planned projects, followed by a discussion and questions proposed by her opponent, Dr. Hana Jungová.

The presentation started with a short background introduction to optical scattering techniques and nanoparticle characterization techniques, followed by an introduction and description of the first paper, “Dual-Angle Interferometric Scattering Microscopy for Optical Multiparametric Particle Characterization,” and, in the end, a brief description of the projects in which Berenice is involved.

In the last section, she outlined the proposed continuation of her PhD: quantification and characterization of biomolecular condensates and their evolution over time, monitoring lipid droplets during long timescales inside living cells, and parametrization for core-shell particles.

Invited Talk by Yu-Wei Chang in the group meeting of Prof. Michael Strano, Department of Chemical Engineering, Massachusetts Institute of Technology, USA, 23 Feb 2024

Working principles for training neural networks with highly incomplete dataset: vanilla (upper panel) vs GapNet (lower panel) *(Image by Yu-Wei Chang.)*

GapNet: Neural network training with highly incomplete datasets

Yu-Wei Chang

Presentation in group meeting of Prof. Michael Strano, Department of Chemical Engineering, Massachusetts Institute of Technology, USA and DiSTAP, Singapore-MIT Alliance for Research and Technology, Singapore.
Date: 23 February 2024

Neural network training requires complete data. We have introduced GapNet, which can train neural networks with incomplete data, using medical data. This approach can be generalized for integrating spectrum data across different frequency ranges, allowing the neural network to combine important information from diverse spectrum datasets.

Colloquium by G. Volpe at the Mini-Symposium with Giovanni Volpe and Pawel Sikorski, Lund, 11 January 2024

Deep Learning for Imaging and Microscopy
Giovanni Volpe
Mini-Symposium with Giovanni Volpe and Pawel Sikorski, Lund, Sweden, 11 January 2024
Date: 11 January 2024
Time: 15:15

Fredrik Skärberg presented his half-time seminar on 10 January 2024

Fredrik Skärberg (right) and opponent Prof. Rebecka Jörnsten (left). *(Photo by A. Ciarlo)*

Fredrik Skärberg completed the first half of his doctoral studies and he defended his half-time on the 10th of January 2024.

The presentation, with title: “Holographic characterization of biological nanoparticles using deep learning”, was held in hybrid format, with part of the audience in the Nexus room and the rest connected through zoom. The half-time consisted in a presentation about his past and planned projects and it was followed by a discussion and questions proposed by his opponent Prof. Rebecka Jörnsten.

The presentation started with a short background to characterization of biological particles inside cells and an introduction to the papers included in the half-time.

It continued with images and videos of various particle types inside cells, both tracked and characterized, followed by a description of the LodeSTAR-model.

In the last section, he outlined the proposed continuation of his PhD, with an ongoing project for monitoring lipid droplets during long timescales and a neural network for 3D rotation parameter estimation of rotating biological samples.

PhD Student: Fredrik Skärberg
Supervisor: Daniel Midtvedt
Co-supervisors: Giovanni Volpe, Fredrik Höök

Fredrik Skärberg and audience in Nexus. *(Photo by A. Ciarlo.)*

Emiliano Gómez presented his half-time seminar on 29 November 2023

Emiliano Gomez Ruiz during his half-time seminar. *(Photo by L. Pérez García.)*

Emiliano Gómez completed the first half of his doctoral studies and he defended his half-time on the 29th of November 2023.

The presentation was conducted in a hybrid format, with part of the audience present in the Nexus room and the remainder connected through Zoom. The seminar comprised a presentation covering both his completed and planned projects, followed by a discussion and questions posed by his opponent, Prof. Martin Adiels.

The presentation commenced with an overview of his concluded projects. The first project with title “Brain Analysis using Graph Theory 2” is a software that uses Deep Learning and Graph Theory to analyse brain networks, this software is an open-source MATLAB with github “github.com/braph-software/BRAPH-2” and two projects in which this software was applied, first one on haematopoietic cell structural pattern taken from bone marrow and the second one is of memory capacity of aging brain networks using reservoir computing.

Talk by G. Volpe at the Symposium on AI, Neuroscience, and Aging, Stockholm, 27 November 2023

Deep Learning for Imaging and Microscopy
Giovanni Volpe
Symposium on AI, Neuroscience, and Aging, Stockholm, Sweden, 27 November 2023
Date: 27 November 2023
Time: 15:55

Video microscopy has a long history of providing insights and breakthroughs for a broad range of disciplines, from physics to biology. Image analysis to extract quantitative information from video microscopy data has traditionally relied on algorithmic approaches, which are often difficult to implement, time consuming, and computationally expensive. Recently, alternative data-driven approaches using deep learning have greatly improved quantitative digital microscopy, potentially offering automatized, accurate, and fast image analysis. However, the combination of deep learning and video microscopy remains underutilized primarily due to the steep learning curve involved in developing custom deep-learning solutions. To overcome this issue, we have introduced a software, DeepTrack 2.1, to design, train and validate deep-learning solutions for digital microscopy. We use it to exemplify how deep learning can be employed for a broad range of applications, from particle localization, tracking and characterization to cell counting and classification. Thanks to its user- friendly graphical interface, DeepTrack 2.1 can be easily customized for user-specific applications, and, thanks to its open-source object-oriented programming, it can be easily expanded to add features and functionalities, potentially introducing deep-learning-enhanced video microscopy to a far wider audience.

Seminar by C. Reichhardt on 30 November 2023

Complex Dynamics in Active Matter Systems, Frustration Effects, Magnus Forces and Synchronization
Charles Reichhardt
Los Alamos National Laboratory

30 November 2023, 16:30, Nexus

Active matter denotes systems with self-propulsion and arises in biological, soft, robotic, and social settings [1]. Here, we outline some of our group’s recent efforts in active systems, including active matter interacting with ordered and disordered substrates, where various kinds of active clogging and commensuration effects can occur that have connections with frustrated systems and Mott physics. We also discuss chiral active systems with a Magnus force, where we find edge currents similar to those found for topological systems or charged particles in magnetic fields. In the presence of quenched disorder, the chiral active system also shows side jump effects with an active matter Hall angle. Finally, we discuss coupled active matter swarmulators where, in addition to activity, the particles have an internal degree of freedom that can become synchronized or antisynchronized. This system shows a variety of new kinds of motility-induced phase-separated states, including active matter stripes, frustrated states, gels, cluster fluids, and glassy states.

[1] Active Brownian particles in complex and crowded environments, Clemens Bechinger, Roberto Di Leonardo, Hartmut Lowen, Charles Reichhardt Giorgio Volpe, and Giovanni Volpe, Reviews of Modern Physics 88 045006 (2016).