Current Herchel Smith Postdoctoral Fellows

Herchel Smith Postdoctoral Fellows
Dr Alyson Ashe Dr Clément Baruteau Dr Camille Bonvin
Dr Libby Caygill Dr Cristina Cotobal Martín Dr Anna Drews
Dr Philip Goodwin Dr Abderrhamane Kaidi Dr Chan Woo Kim
Dr Wansu Kim Dr Yanki Lekili Dr Gareth Lloyd
Dr Claire Lye Dr Pedro Machado Dr Kei Miyamoto
Dr Annabel Murphy Dr Vijay Narayan Dr Josana Rodriguez Sánchez
Dr Alexandra Sapetschnig Dr Alfonso Sorrentino Dr Yasuhiro Takashima
Dr Alfonso Sorrentino Dr Brian Walker

Dr Alyson Ashe, 2009

Email: aa597 at cam.ac.uk




Clément Baruteau

Dr Clément Baruteau, 2010

My research activities cover various aspects of the formation and evolution of planetary systems and the dynamics of astrophysical discs, with a special emphasis on the interaction between planets and their nascent protoplanetary disc (planetary migration). My research interests are also directed toward applying theories of disc-planet interactions, and more generally astrophysical fluid dynamics methods to various astrophysical contexts, including star-planet tidal interactions.


Email: C.Baruteau at damtp.cam.ac.uk




Camille Bonvin

Dr Camille Bonvin, 2010

My research field is cosmology, with special emphasis on the problem of the accelerated expansion of the Universe. In the last decades, it has become clear that our theoretical description of the Universe fails to interpret correctly the observations if we adopt Einstein’s theory as the theory of gravity and the Standard Model of particle physics as the theory of matter. For example baryonic matter is not sufficient to explain gravitational interactions in structures like galaxies and clusters of galaxies. Furthermore, observations seem to indicate that the Universe is undergoing a phase of accelerated expansion that cannot be driven by known matter or energy. Two directions are currently explored to solve these problems: either one invokes the presence of new exotic forms of matter (dark matter) and energy (dark energy), or one attempts to modify Einstein’s theory of gravity at galactic and cosmological scales. In this context, my research addresses the problem of the accelerated expansion of the Universe from two angles. From an observational point of view, I am working on gravitational lensing and on the luminosity distance of supernovae. More precisely, I am interested in the information that these observations carry on the mechanism responsible for the accelerated expansion of the Universe. On the other hand, from a more theoretical point of view, I am studying new models of dark energy and modified gravity with the goal of constraining them, either by analysing the internal consistency of the theories or by confronting them with observations.

Email: cbonvin at ast.cam.ac.uk




Libby Caygill



Dr Libby Caygill, 2009

I'm interested in the control of neural stem cell behaviour by non-coding RNAs. I’m currently working in the lab of Prof Andrea Brand. Using the Drosophila melanogaster optic lobe as a model I aim to determine whether non-coding RNAs play a role in determining whether neural stem cells divide in a symmetric manner, increasing the stem cell pool, or in an asymmetric manner, producing differentiated neurons. .



Email: e.caygill at gurdon.cam.ac.uk




Dr Cristina Cotobal Martín, 2011

The study of the genome-wide networks that regulate gene expression at the posttranscriptional level: Functional genomics; Transcriptional and Posttranscriptional regulation; Fission yeast.

Email: cc606 at cam.ac.uk



Anna Drews

Dr Anna Drews, 2012

After my study of biology I graduated in 2006 from the University of Göttingen (Germany). During my diploma thesis I worked on the ecology and morphology of hover flies in different habitats and their anti-predator colouration. Afterwards I did my Ph.D. at the Institute of Pharmacology and Toxicology at the University of Saarland (Homburg/Germany). The main scientific training was in electrophysiology (patch clamp), with focus on function and biophysics of TRP channels in mouse, rat and Drosophila. Furthermore, I was a member of the graduate research school ‘Calcium-Signalling and Cellular Nanodomains’ (GK 1326). In 2010 I worked as research assistant in the Department of Physiology at the same University. The research focused on the communication between neurons. Since march 2011 I have a postdoctoral position in Prof. Klenermans group in the Department of Chemistry where I started research in the SICM field. In October 2012 I became a Bye-Fellow of Newnham College. Besides biology I am interested in astronomy, egyptology and dancing.

Email: add34 at cam.ac.uk




Philip Goodwin

Dr Philip Goodwin, 2011

After receiving an MSci in Physics from Imperial College in 2003, I gained a PhD in Earth Sciences from the University of Liverpool in 2008, where my work focussed on the carbon cycle. My postdoctoral research career began at the School of Environmental Sciences at UEA, Norwich. I now hold both Herchel Smith and NERC Postdoctoral Fellowships at the Department of Earth Sciences, Cambridge, where I investigate how best to combine observational evidence and numerical models to constrain recent glacial-interglacial cycles in atmospheric carbon dioxide. I am currently a fellow of Wolfson College, Cambridge.

Combining paleo-proxies with numerical models to constrain past environments
I am motivated by the question: ‘How can geochemical observations of past conditions best be combined with numerical climate models to reconstruct past environments?’ It is impossible to measure directly the climate variables of the past, such as temperature and rainfall. However, various observable proxies can be measured, such as isotopic ratios in deep-sea sediments, which give clues to past climates. To reconstruct past climates and ocean states, measured proxies are compared against simulated proxies in numerical climate models. The goal for the modeller is to achieve a simulation in which the measured and simulated proxies are in agreement. This methodology can have misleading results because the conditioning of the system is neglected.

I have shown that using measurements of palaeo-proxies to constrain numerical simulations of past environments is equivalent to performing a matrix transformation. This matrix transformation converts directly from measured proxy values to simulated environmental variables. If the matrix is ill-conditioned then accurately simulated proxies still result in inaccurately simulated environmental variables. For a given set of environmental variables, each possible combination of proxies that could constrain the system results in a different matrix. By evaluating the error propagation through the matrices, the optimum combination of proxies can be found. I propose a methodology in which modellers evaluate the matrices in order to find which proxy measurements are required to constrain a particular set of environmental variables. The results of such a study could then inform geochemists what to measure to address a specific problem in palaeoceanography.

Email: pag46 at cam.ac.uk




Dr Abderrhamane Kaidi, 2009

The effect of chromatin structure on DNA repair.

Email: a.kaidi at gurdon.cam.ac.uk

 



Chan Woo Kim


Dr Chan Woo Kim, 2010

The areas of my research are in the field of applied pde. I have been studying two different types of problems : boundary problems of the Boltzmann equation and the stability/instability of free boundary problem in fluid dynamics. Now I start to study large amplitude solutions of the Boltzmann equation with Clement Mouhot.


Email: cwk29 at cam.ac.uk




Wansu Kim


Dr Wansu Kim, 2011

My research topic is algebraic number theory and algebraic geometry, and my recent focus is p-adic Hodge theory and p-divisible groups.


Email: W.Kim at dpmms.cam.ac.uk




Yanki Lekili



Dr Yanki Lekili, 2010

Geometry.


Email: Y.Lekili at dpmms.cam.ac.uk




Dr Gareth Lloyd, 2009

I was born in Harare, Zimbabwe. After completing high school at St. John’s College (Harare, Zimbabwe) in 1997, I first followed my dream of being a professional runner in Stellenbosch, South Africa. I, eventually, started my studies at the University of Stellenbosch in 2000. At the end of my honours year I meet Prof. Len Barbour, with whom I then did an MSc, titled “Crystal Engineering of Porosity”. I received the S2A3 Bronze Medal from the Southern Africa Association for the Advancement of Science for the thesis. After obtaining a Commonwealth Scholarship to study a Ph.D. in the U.K., I went to Durham University to work with Prof. Jon Steed. I received my Ph.D. in 2010, titled “Anion-Tuning of Supramolecular Gel Properties”. I currently hold a Herschel Smith Post-Doctoral Research Fellowship in Inorganic Materials in the Chemistry Department, Cambridge.

Email: gol20 at cam.ac.uk




Claire Lye

Dr Claire Lye, 2010

As an undergraduate I studied Natural Sciences at Queens’ College, Cambridge, specialising in cell and developmental biology (2001-2004). I completed my PhD in developmental biology at the Institute of Child Health, University College London (2004-2008). I now work in the Department of Physiology, Development and Neuroscience in Dr Bénédicte Sanson’s group and and collaborate with Dr Guy Blanchard, Dr Richard Adams and Dr Alexander Kabla. My current research focuses on how groups of cells move and change shape to achieve the diverse array of tissue shapes seen within animal bodies. Additionally I am a Research Fellow at Magdalene College and have undertaken undergraduate teaching on behalf of Peterhouse College.

Research Interests
Embryonic development requires both cell differentiation and tissue morphogenesis. Cell differentiation is the process by which cells develop the specialised characteristics required for their function. Tissue morphogenesis is the development of form and structure, and is also important for function. Gaining a deeper understanding of morphogenetic mechanisms is relevant to human health in three areas. First, it should lead to a better understanding of birth defects, which are now the leading cause of infant mortality in developed countries. Second, it will increase our understanding of cancer metastasis: there is evidence that many cancers invade healthy tissues through collective cell movements that are very reminiscent of embryonic morphogenetic movements. Finally, it will help the development of regenerative medicine: tissue and organ engineering will require in-depth knowledge of morphogenetic mechanisms to be able to build three-dimensional structures following stem cell manipulation.

It is known that the complex shapes of tissues and organs are achieved in part by the active behaviours of their constituent cells. However, since tissues do not develop in isolation, other morphogenetic events occurring nearby almost certainly influence the shape of a given tissue by inducing passive changes. Active cell behaviours have been the focus of the majority of morphogenesis research, and progress has been made in understanding how the active behaviours of cells shape tissues through the production of intrinsic forces. A much less explored area is how the forces extrinsic to a tissue influence its final shape.

I am using the early Drosophila (fruit-fly) embryo to address this question. A key benefit of this model system is that in early Drosophila embryos morphogenetic events very like those observed in mammals occur in a short time window. I hope to discover fundamental mechanisms of how extrinsic forces shape developing tissues. Drosophila are amenable to genetic manipulation so different morphogenetic events can be prevented genetically in order to assess the contribution of those events to final tissue shape. Since living Drosophila embryos can be imaged as they develop using microscopy I will capture detailed movies of cell behavior over time in both normal and abnormal embryos. I will then use the computational and mathematical tools developed by my collaborators to analyse thoroughly the movement and shape changes of thousands of cells. This will allow me to identify the forces produced by different morphogenetic events and to assess how these forces influence the shapes of different tissues in the embryo.

I hope that this approach will lead to a better understanding of the mechanisms underlying the morphogenesis of animal tissues.

Email: cmg38 at cam.ac.uk




Pedro Machado

Dr Pedro Machado, 2010

I am the lab's house physicist. My doctoral work was in the field of theoretical high energy physics, where I investigated the scale-dependent behaviour of one of our putative theories of quantum gravity with the aim of understanding how physical processes occurring at the submicroscopic scale interact and integrate to generate our observed, large-scale universe. After completing my PhD, I decided to move my research towards quantitative biology and, more specifically, morphogenesis. While my present field is a long way away from my previous work in terms of content, both share a general underlying question - how does the coordinated, large-scale behaviour of a system emerge from the cross-interactions of its parts? In morphogenesis, this question becomes the challenge of understanding how the development and maintenance of whole organisms arise from the interplay of molecular and cellular processes that occur at various time and length scales.

Dorsal Closure provides a powerful model system for addressing this issue. To this effect, we are investigating how subcellular forces generate cell shape changes that combine to orchestrate coherent tissue deformation, and how these cell shape changes and tissue constraints in turn regulate the subcellular forces. Our work, in collaboration with G. Blanchard, from the Department of PDN in Cambridge, and Nicole Gorfinkiel, from the Center for Molecular Biology in the Universidad Autonoma de Madrid, involves a combination of imaging analysis, theoretical modelling and computer simulations. Specifically, we are first analysing the relation between strain and stress in amnioserosa cells at the cellular and subcellular level with the aim of building a phenomenological model of DC dynamics and specifying its material properties. This phenomenological description is then used to constrain and guide the development of discrete models of cytoskeleton activity and to quantify the relevant microscopic parameters. Lastly, these results are combined to inform Monte Carlo simulations of Dorsal Closure.

Email: p.farias-machado at gen.cam.ac.uk




Dr Kei Miyamoto, 2011

Email: km518 at cam.ac.uk




Annabel Murphy


Dr Annabel Murphy, 2011

My interests lie in facilitating the use of microorganisms for the production of useful chemicals, and in particular antibiotics, from renewable feedstocks. After completing a PhD in natural product synthesis in New Zealand (funded by a Commonwealth Scholarship), I joined Prof. Simpson's group at the University of Bristol as a post-doctoral researcher. There I studied the biosynthesis of two related antibiotics and used mutant microorganisms to generate potent, new antibiotics. My current research, undertaken within the group of Prof. Leadlay, aims to facilitate the production of 'unnatural' compounds by microorganisms, by probing a biosynthetic enzyme that naturally has a broad substrate tolerance.

Email: acm95 at cam.ac.uk




Dr Vijay Narayan, 2011

Email: vn237 at cam.ac.uk




Josana Rodriguez Sánchez

Dr Josana Rodriguez Sánchez, 2011

Cell polarity is defined as an asymmetry within the cell, for example protein distribution, cell division and cell shape. The establishment of polarity within a cell or tissue is an essential process during the development of an organism. In the case of C. elegans nematode, the first embryonic cell division must be asymmetric generating a larger anterior daughter cell. The C. elegans embryo is polarized by an unknown cue in the sperm centrosome. In response to this cue the acto-myosin cortical network moves towards the anterior pole of the embryo promoting the anterior localization of the PDZ containing proteins PAR-3 and PAR-6 together with PKC-3 (atypical protein kinase-C), while PAR-2 and PAR-1 (serine-threonine kinase) become enriched at the posterior. These two protein complexes mutually antagonize each other to maintain their asymmetric locations at the cortex. PAR-4 (serine-threonine kinase) and PAR-5 (14-3-3 protein), uniformly distributed at the cortex, are also required for embryo polarity. PAR proteins control important aspects of the C. elegans first asymmetric cell division such as orientation and posterior displacement of the mitotic spindle, cell cycle timing and differential distribution of cell fate determinants (Galli and van den Heuvel, 2008). If the polarity of this first cell division is disrupted, the embryo divides symmetrically and further divisions are abnormal causing embryonic lethality. The transparency of the embryo and powerful genetic tools amenable to C. elegans has allowed the rapid identification of proteins required for this first asymmetric cell division, among them the PAR proteins.

PAR proteins and most other proteins shown to be involved in C. elegans cell polarity are conserved in humans and have similar functions in other model organisms. This argues in favour of conserved polarity mechanisms. However, understanding how these proteins control cell polarity remains an open question in the field and very few targets of PAR proteins have been identified. In order to identify new genes and new genetic interactions (functional relationships between these genes) involved in polarity we are performing large-scale RNA interference (RNAi) screens in C. elegans using different polarity mutant backgrounds.

Email: j.rodriguez at gurdon.cam.ac.uk




Dr Alexandra Sapetschnig, 2010

Email: as878 at cam.ac.uk




Alfonso Sorrentino



Dr Alfonso Sorrentino, 2008

Research Interests: Hamiltonian and Lagrangian systems, symplectic geometry.

Email: A.Sorrentino at dpmms.cam.ac.uk




Dr Yasuhiro Takashima, 2009

Email: yt269 at cam.ac.uk




Brian Walker

Dr Brian Walker, 2011

I am broadly interested in the physics, materials science, and chemistry of electronic materials, and I am motivated to understand these materials in a way that enables the transition to a sustainable economy. My interests include:
1. learning the fundamental characteristics of materials that make them suitable for energy harvesting.
2. assembling devices to test our hypothetheses.
3. developing new, more sustainable means to make optoelectronic devices.

Both organic and inorganic materials have properties that make them suited for use in semiconductor devices, but controlling or even studying interfaces--within a material as well as between separate materials--is an ongoing challenge. Currently I study the physics of organic semiconductors at the interface of inorganic semiconductor nanocrystals in the Optoelectronics Group in the Cavendish Laboratory, and my interest in this problem grew out of my doctoral research at MIT. One challenge that is particularly interesting to me at the moment is the development of a basic mechanism for singlet fission in organic semiconductors.

Email: bjw53 at cam.ac.uk