Quantum and Classical Molecular Dynamics

PGR-P-109

Key facts

Type of research degree: PhD
Application deadline: Ongoing deadline
Project start date: Sunday 1 October 2023
Country eligibility: International (open to all nationalities, including the UK)
Funding: Competition funded
Supervisors: Professor Dmitry Shalashilin
Schools: School of Chemistry

<h2 class="heading hide-accessible">Summary</h2>

The goal of our research is to develop new computational methods for atomistic simulations in chemistry and physics. These methods should allow us to treat bigger molecular systems faster and more accurately.

<h2 class="heading hide-accessible">Full description</h2>

There are two main areas of research in the Leeds Quantum and Classical Molecular Dynamics group.    <a href="https://molecular-dynamics.leeds.ac.uk/research/">Multidimensional Quantum Mechanics</a> The first project is focused on quantum wave packet dynamics.  Chemical dynamics is about rearranging nuclei whose motion is often nonclassical.  Such effects as transitions between electronic states of molecules, tunnelling, zero point energy, and quantization of vibrational and rotational motions are crucial for understanding chemical dynamics.  Although the lows of quantum mechanics are known quantum equations for realistic systems with many degrees of freedom are very difficult to solve even with the fastest computers.  The central problem is that complicated quantum wave functions are always represented as a superposition of a large number of simple basis functions and the size of the basis grows extremely fast with the number of degrees of freedom.  We develop new techniques which speed up quantum simulations and allow to treat larger molecular systems [1-3]. We developed several methods which exploit very simple idea of guiding basis set functions with trajectories and applied them to many interesting problems in chemistry and physics which range from chemical dynamics [4] and spectroscopy to dynamics of electrons in laser field [5] and even quantum computers [6]. <a href="https://molecular-dynamics.leeds.ac.uk/research/">Accelerated Classical Mechanics</a> The second project is focused on classical molecular dynamics of biological molecules such as proteins for example.  Here we disregard quantum effects and only consider classical dynamics.  The molecules we are simulating are often comprised of thousands of atoms, which are viewed almost as classical balls connected by springs.  The problem with classical molecular dynamics is that for molecules of this size atomistic simulations can be done on the time scale of picoseconds but the time scale of important biological processes such as protein folding for example is microseconds or longer so that at least 6 orders of magnitude of time scale have to be bridged.  We developed efficient methods which allow to solve this problem by viewing long time dynamics as a set of short time processes.  Therefore one very long simulation is replaced by a number of short ones.  An example of such study can be found in ref [7] where we reproduced experimental data on peptide cyclization. With our new methods of accelerated classical dynamics we are looking now at protein folding, drug binding and other problems important in biochemistry in which we reach relevant time scales [7].  References [1] Shalashilin, D.V., Child, M.S. Chem. Phys. 304, 103 (2004);  [2] Shalashilin, D.V. , Burghardt, I.  J. Chem. Phys. 128, 084104 (2008); [3] Shalashilin, D.V. J. Chem. Phys. 132, 244111 (2010); [4] Makhov, D.V., K.Saita, Martinez T.J., Shalashilin,  D.V. ,Phys.Chem.Chem.Phys., 17, 3316 (2015); [5] Kirrander, A., Shalashilin, D.V. Phys. Rev. A 84, 033406 (2011); [6]. Sai-Yun Ye, Shalashilin D.V., Serafini A. Phys. Rev. A 86, 032312 (2012); [7] (a) Glowacki, D. R.; Paci, E.; Shalashilin, D. V. J Phys Chem B 113 16603 (2009);  (b) D.V. Salashilin,G.Beddard, E. Paci and D. R. Glowacki, J. Chem. Phys. 137 165102 (2012).

<h2 class="heading">How to apply</h2>

Formal applications for research degree study should be made online through the <a href="https://www.leeds.ac.uk/info/130206/applying/91/applying_for_research_degrees">University's website</a>. Please state clearly in the Planned Course of Study that you are applying for PHD Chemistry FT and in the research information section that the research degree you wish to be considered for is Quantum and Classical Molecular Dynamics as well as <a href="https://physicalsciences.leeds.ac.uk/staff/197/professor-dmitry-shalashilin">Professor Dmitry Shalashilin</a> as your proposed supervisor. If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below). As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability. Applications will be considered on an ongoing basis.  Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application.  We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed. Please note that you must provide the following documents at the point you submit your application: <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> <li>Funding information including any alternative sources of funding that you are applying for or if you are able to pay your own fees and maintenance</li> </ul>

<h2 class="heading heading--sm">Entry requirements</h2>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

<h2 class="heading heading--sm">English language requirements</h2>

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<h2 class="heading">Funding on offer</h2>

Self-Funded or externally sponsored students are welcome to apply. UK – The <a href="https://phd.leeds.ac.uk/funding/209-leeds-doctoral-scholarships-2022">Leeds Doctoral Scholarships</a> and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> are available to UK applicants (open from October 2023). <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. Non-UK –The <a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a> is available to nationals of China (open from October 2023). The <a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a> is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. Important:  Any costs associated with your arrival at the University of Leeds to start your PhD including flights, immigration health surcharge/medical insurance and Visa costs are not covered under these studentships. Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.

<h2 class="heading">Contact details</h2>

For further information about this project, please contact Professor Dmitry Shalashilin: e:  <a href="mailto:D.Shalashilin@leeds.ac.uk">D.Shalashilin@leeds.ac.uk</a> For further information about your application, please contact Doctoral College Admissions: e:  <a href="mailto:maps.pgr.admissions@leeds.ac.uk">maps.pgr.admissions@leeds.ac.uk</a>